U.S. patent application number 15/155675 was filed with the patent office on 2016-11-17 for methods for restoring microbiota of newborns.
This patent application is currently assigned to University of Puerto Rico. The applicant listed for this patent is New York University, University of Puerto Rico. Invention is credited to Maria Gloria DOMINGUEZ-BELLO.
Application Number | 20160331792 15/155675 |
Document ID | / |
Family ID | 57249409 |
Filed Date | 2016-11-17 |
United States Patent
Application |
20160331792 |
Kind Code |
A1 |
DOMINGUEZ-BELLO; Maria
Gloria |
November 17, 2016 |
METHODS FOR RESTORING MICROBIOTA OF NEWBORNS
Abstract
The invention relates to methods and compositions for restoring
normal microbiota in pre-term newborns or newborns delivered by
Cesarean section and methods for preventing or ameliorating
diseases associated with delivery by Cesarean section or pre-term
birth comprising administering to said newborns at the time of
birth or shortly thereafter an effective amount of a vaginal
microbiota inoculum obtained from the newborn's mother or a donor
or an effective amount of a probiotic composition.
Inventors: |
DOMINGUEZ-BELLO; Maria Gloria;
(New York, NY) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
University of Puerto Rico
New York University |
San Juan
New York |
NY |
PR
US |
|
|
Assignee: |
University of Puerto Rico
San Juan
NY
New York University
New York
|
Family ID: |
57249409 |
Appl. No.: |
15/155675 |
Filed: |
May 16, 2016 |
Related U.S. Patent Documents
|
|
|
|
|
|
Application
Number |
Filing Date |
Patent Number |
|
|
62161549 |
May 14, 2015 |
|
|
|
Current U.S.
Class: |
1/1 |
Current CPC
Class: |
A61K 35/747 20130101;
A61K 35/741 20130101; A61K 35/742 20130101; A61K 35/745 20130101;
A61P 37/00 20180101 |
International
Class: |
A61K 35/747 20060101
A61K035/747; A61K 35/745 20060101 A61K035/745; A61K 35/741 20060101
A61K035/741 |
Goverment Interests
STATEMENT AS TO FEDERALLY SPONSORED RESEARCH
[0002] The United States Government has certain rights to this
invention by virtue of funding reserved from Grant No. R01 DK090989
from the National Institutes of Health.
Claims
1. A method for restoring normal microbiota in an infant delivered
by Cesarean section or in a pre-term infant, said method comprising
administering to said infant at the time of birth and/or within the
first 4 months of life an effective amount of a probiotic
composition, wherein said probiotic composition (i) stimulates
growth and/or activity of bacteria which are under-represented in
microbiota of said infant as compared to vaginally delivered
full-term infants, and/or (ii) inhibits growth and/or activity of
bacteria which are over-represented in microbiota of said infant as
compared to vaginally delivered full-term infants.
2. The method of claim 1, wherein said probiotic composition
comprises one or more bacterial strains from one or more taxa
selected from the group consisting of Bacteroides, Lactobacillus,
Bifidobacterium, Bacteriodales, Parabacteroides, Bacteroidacea,
Porphyromonadaceae, Coriobacteriales, Clostridiaceae,
Stenotrophomonas, and Gemella.
3. The method of claim 1, wherein said probiotic composition
comprises one or more bacterial strains from one or more taxa
recited in Table 1A.
4. The method of claim 1, wherein said probiotic composition
comprises one or more bacterial strains from one or more species
recited in Table 1B.
5. The method of claim 1, wherein said probiotic composition
comprises one or more bacterial strains which can be found in a
healthy vaginal microbiota from a pregnant woman in the third
trimester of pregnancy before or at the time of giving birth.
6. The method of claim 1, wherein said probiotic composition
comprises one or more components selected from the group consisting
of live bacterial cells, conditionally lethal bacterial cells,
inactivated bacterial cells, killed bacterial cells, spores,
recombinant carrier strains, cell extract, and bacterially-derived
products.
7. The method of claim 1, wherein said probiotic composition
comprises (i) a carrier and/or excipient and/or (ii) one or more
prebiotic agents which stimulate growth and/or activity of one or
more bacteria present in the composition.
8. The method of claim 1, wherein the probiotic composition is
delivered to the infant in a form of a liquid, foam, cream, spray,
powder, or gel.
9. A method for restoring normal microbiota in an infant delivered
by Cesarean section or in a pre-term infant, said method comprising
administering to said infant at the time of birth and/or within the
first 4 months of life an effective amount of a vaginal microbiota
inoculum, wherein said inoculum is obtained from the subject's
mother or from a donor during the third trimester of pregnancy
before or at the time of giving birth.
10. The method of claim 9, wherein the vaginal microbiota inoculum
is delivered to the infant in a form of a liquid, foam, cream,
spray, powder, or gel.
11. The method of claim 9, wherein the vaginal microbiota inoculum
is obtained and/or delivered using an absorbent material or
device.
12. The method of claim 11, wherein the vaginal microbiota inoculum
is transferred to said absorbent material or device by introducing
said absorbent material or device in vagina prior to the birth or
at the time of Cesarean section.
13. The method of claim 9, further comprising monitoring the
infant's microbiota after the administration of the vaginal
microbiota inoculum by: (a) determining a relative abundance of one
or more bacterial taxa in a microbiota sample obtained from the
infant, and (b) comparing the relative abundance(s) determined in
step (a) to (i) a predetermined standard value or (ii) to the
abundance(s) of the same taxa in a control subject or (iii) to the
average value of abundances of the same taxa in several control
subjects.
14. The method of claim 13, wherein the control subject is a
vaginally delivered full-term healthy infant.
15. A method for treating a disease in a subject associated with
the subject's delivery by Cesarean section or with the subject's
premature birth, said method comprising administering to said
subject at the time of birth and/or within the first 4 months of
life a therapeutically effective amount of a vaginal microbiota
inoculum, wherein said inoculum is obtained from the subject's
mother or from a donor during the third trimester of pregnancy
before or at the time of giving birth.
16. The method of claim 15, wherein said disease is an inflammatory
or an autoimmune disorder.
17. The method of claim 15, wherein the vaginal microbiota inoculum
is delivered to the subject in a form of a liquid, foam, cream,
spray, powder, or gel.
18. The method of claim 15, wherein the vaginal microbiota inoculum
is obtained and/or delivered using an absorbent material or
device.
19. The method of claim 18, wherein the vaginal microbiota inoculum
is transferred to said absorbent material or device by introducing
said absorbent material or device in vagina prior to the birth or
at the time of Cesarean section.
20. The method of claim 15, further comprising monitoring the
subject's microbiota after the administration of the vaginal
microbiota inoculum by: (a) determining a relative abundance of one
or more bacterial taxa in a microbiota sample obtained from the
infant, and (b) comparing the relative abundance(s) determined in
step (a) to (i) a predetermined standard value or (ii) to the
abundance(s) of the same taxa in a control subject or (iii) to the
average value of abundances of the same taxa in several control
subjects.
21. The method of claim 20, wherein the control subject is a
vaginally delivered full-term healthy infant.
22. A method for treating a disease in a subject associated with
the subject's delivery by Cesarean section or with the subject's
premature birth, said method comprising administering to said
subject at the time of birth and/or within the first 4 months of
life a therapeutically effective amount of a probiotic composition,
wherein said probiotic composition (i) stimulates growth and/or
activity of bacteria which are under-represented in microbiota of
said subject as compared to vaginally delivered full-term infants,
and/or (ii) inhibits growth and/or activity of bacteria which are
over-represented in microbiota of said subject as compared to
vaginally delivered full-term infants.
23. The method of claim 22, wherein said disease is an inflammatory
or an autoimmune disorder.
24. The method of claim 22, wherein said probiotic composition
comprises one or more bacterial strains from one or more taxa
selected from the group consisting of Bacteroides, Lactobacillus,
Bifidobacterium, Bacteriodales, Parabacteroides, Bacteroidacea,
Porphyromonadaceae, Coriobacteriales, Clostridiaceae,
Stenotrophomonas, and Gemella.
25. The method of claim 22, wherein said probiotic composition
comprises one or more bacterial strains from one or more taxa
recited in Table 1A.
26. The method of claim 22, wherein said probiotic composition
comprises one or more bacterial strains from one or more species
recited in Table 1B.
27. The method of claim 22, wherein said probiotic composition
comprises one or more bacterial strains which can be found in a
healthy vaginal microbiota from a pregnant woman in the third
trimester of pregnancy before or at the time of giving birth.
28. The method of claim 22, wherein said probiotic composition
comprises one or more components selected from the group consisting
of live bacterial cells, conditionally lethal bacterial cells,
inactivated bacterial cells, killed bacterial cells, spores,
recombinant carrier strains, cell extract, and bacterially-derived
products.
29. The method of claim 22, wherein said probiotic composition
comprises (i) a carrier and/or excipient and/or (ii) one or more
prebiotic agents which stimulate growth and/or activity of one or
more bacteria present in the composition.
30. The method of claim 22, wherein the probiotic composition is
delivered to the subject in a form of a liquid, foam, cream, spray,
powder, or gel.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application claims priority to U.S. Provisional
Application No. 62/161,549, filed on May 14, 2015, the disclosure
of which is herein incorporated by reference in its entirety.
FIELD
[0003] The application relates to methods for restoring normal
microbiota in pre-term infants or infants delivered by Cesarean
section and methods for preventing or ameliorating diseases
associated with delivery by Cesarean section or pre-term birth
comprising administering to said infants at the time of birth or
shortly thereafter an effective amount of a vaginal microbiota
inoculum obtained from the infant's mother or a donor during the
third trimester of pregnancy before or at the time of giving birth
or an effective amount of a probiotic composition, wherein said
probiotic composition (i) stimulates growth and/or activity of
bacteria which are under-represented in microbiota of said newborn
as compared to vaginally delivered full-term newborns, and/or (ii)
inhibits growth and/or activity of bacteria which are
over-represented in microbiota of said newborn as compared to
vaginally delivered full-term newborns. Also provided are methods
for diagnosing abnormal microbiota development in a newborn,
comprising determining a relative abundance of one or more
bacterial taxa in a microbiota sample obtained from said
newborn.
BACKGROUND
[0004] Maternal vaginal microbes provide the natural seeding to the
newborn microbiota (1). Whether vaginal microbes can reach the
placenta and the fetus before labor initiates, still unclear (2,
3), but mode of delivery overwhelms any other possible previous
signal, and C-section-born babies are microbiologically different
from vaginally born infants (1). The maternal vaginal (4) and
intestinal (5) microbiota change during the third trimester of
pregnancy, but the significance of these changes for the fitness of
the baby has not been understood. Early interaction with indigenous
microbes is essential for healthy immunological and metabolic
programming, and contact with bacterial populations in the vagina
during birth marks the beginning of eventual massive bacterial
colonization of the newborn's mucosal surfaces. Mucosal immunity is
strongly influenced by the microbiota (6), which in the gut mucosa,
is subject to continuous surveillance by M cells--from the Peyer's
patches of the gut-associated lymphoid tissue (GALT)--for
processing by local dendritic cells and subsequently modulate CD4+
to produce Tregs and induce tolerance.
[0005] The "education" of the immune system by the microbiota
starts at the very first microbial exposure and pioneer bacteria
probably play a determinant role. Few studies have focused on the
development of the intestinal microbiota and immunity (7-10), but
the assembly in multiple body sites, the fate of vaginal lactic
acid bacterial populations, and the ecological dynamics between
maternal and infant communities that interact are not known.
Despite the vast descriptive knowledge about the microbiota of
American adults generated by the HMP project (NIH), little is known
about developmental aspects of the microbiota.
[0006] The incidence of immune, inflammatory, and metabolic
disorders is increasing in industrialized countries (11, 12). Early
life events and aberrant microbial colonization has been associated
with these diseases (12, 13). Epidemiological associations show
C-section delivery increased risk of asthma and allergies (14-21),
intestinal inflammatory conditions (19, 22-24). Obesity and
diabetes (type I) is also increased by C-section birthing (19,
25-29) and by antibiotic consumption (19, 27-30) even as early as
during gestation (25).
[0007] The phenomenon of decreased oral and gut microbial diversity
in the first days after birth, previously reported in mice (36), is
of unknown functional significance, but might be reflecting the
selective effect of milk on the gut microbiota. Bacteroides,
Clostridiales and Bifidobacterium are bacteria that are enriched in
the gut during the first weeks of life, during strict
lactation.
[0008] Cesarean section birthing without maternal membrane rupture,
as in the case of scheduled Cesarean, impedes the seeding of the
babies with vaginal microbes. C-section is medically indicated in
13-15% of the births, saving many lives of mothers and babies.
However, scheduled C-section is becoming the standard of birthing
in many countries of the world, with over 50% of births in Brazil,
Dominican Republic, and Iran and many other countries approaching
these rates (Health at a Glance 2011: OECD Indicators; WHO Global
Health Observatory; (31); (37)). C-section birthing is associated
with short health risks for the mother and baby and with long term
health risks for the babies, including celiac disease (23, 24),
asthma (16, 20, 21, 38), type 1 diabetes (39, 40), and obesity (32,
41, 42).
SUMMARY
[0009] As specified in the Background section above, there is a
great need in the art for preventing or ameliorating diseases
associated with delivery by Cesarean section or pre-term birth. The
present application addresses these and other needs by providing
methods for restoring normal microbiota in pre-term newborns or
newborns delivered by Cesarean section and methods for treating
(e.g., preventing or ameliorating) diseases associated with
delivery by Cesarean section or pre-term birth comprising
administering to said newborns at the time of birth or shortly
thereafter an effective amount of maternal vaginal microbiota
inoculum or an effective amount of a probiotic composition, wherein
said probiotic composition (i) stimulates growth and/or activity of
bacteria which are under-represented in microbiota of said newborn
as compared to vaginally delivered full-term newborns, and/or (ii)
inhibits growth and/or activity of bacteria which are
over-represented in microbiota of said newborn as compared to
vaginally delivered full-term newborns.
[0010] In one aspect, the invention provides a method for restoring
normal microbiota in an infant delivered by Cesarean section, said
method comprising administering to said infant at the time of birth
and/or within the first 4 months of life (preferably, within the
first 24 hours of life, most preferably within the first hour of
life) an effective amount of a vaginal microbiota inoculum, wherein
said inoculum is obtained from the subject's mother or from a donor
during the third trimester of pregnancy before or at the time of
giving birth.
[0011] In a related aspect, the invention provides a method for
restoring normal microbiota in a pre-term infant, said method
comprising administering to said infant at the time of birth and/or
within the first 4 months of life (preferably, within the first 24
hours of life, most preferably, within the first hour of life) an
effective amount of a vaginal microbiota inoculum, wherein said
inoculum is obtained from the subject's mother or from a donor
during the third trimester of pregnancy before or at the time of
giving birth.
[0012] In a further aspect, the invention provides a method for
treating (e.g., preventing or ameliorating) a disease in a subject
associated with the subject's delivery by Cesarean section or with
the subject's pre-term birth, said method comprising administering
to said subject at the time of birth and/or within the first 4
months of life an effective amount of a vaginal microbiota
inoculum, wherein said inoculum is obtained from the subject's
mother or from a donor during the third trimester of pregnancy
before or at the time of giving birth. In one embodiment, said
disease is an inflammatory or an autoimmune disorder. In one
embodiment, said disease is selected from the group consisting of
autoimmune diseases, allergic diseases, infectious diseases, and
rejection in organ transplantations. In one specific embodiment,
said disease is selected from the group consisting of asthma,
allergy, celiac disease, type 1 diabetes, obesity, necrotizing
enterocolitis, inflammatory bowel disease (IBD), ulcerative
colitis, Crohn's disease, sprue, autoimmune arthritis, rheumatoid
arthritis, multiple sclerosis, graft vs. host disease following
bone marrow transplantation, osteoarthritis, juvenile chronic
arthritis, Lyme arthritis, psoriatic arthritis, reactive arthritis,
spondyloarthropathy, systemic lupus erythematosus, insulin
dependent diabetes mellitus, thyroiditis, asthma, psoriasis,
dermatitis scleroderma, atopic dermatitis, graft versus host
disease, acute or chronic immune disease associated with organ
transplantation, sarcoidosis, and atherosclerosis.
[0013] In on embodiment of any of the above methods of the
invention, the vaginal microbiota inoculum is delivered to the
mouth, nose, or skin of the infant. In one embodiment of any of the
above methods of the invention, the vaginal microbiota is inoculum
administered to the infant by a route selected from the group
consisting of oral, topical, rectal, mucosal, sublingual, nasal,
and via naso/oro-gastric gavage. In one embodiment of any of the
above methods of the invention, the vaginal microbiota is
administered to the infant by placing it on the maternal breast
and/or chest.
[0014] In one embodiment of any of the above methods of the
invention, the vaginal microbiota inoculum is delivered to the
infant in a form of a liquid, foam, cream, spray, powder, or gel.
In one embodiment of any of the above methods of the invention, the
vaginal microbiota inoculum is delivered to the infant in a form of
a composition which comprises (i) a carrier and/or excipient and/or
(ii) one or more prebiotic agents which stimulate growth and/or
activity of one or more bacteria present in the composition. In one
specific embodiment, said composition comprises a buffering agent
to adjust pH to the natural vaginal pH at the time of labor or to a
pH of 3.5 to 7. In one specific embodiment, said composition
comprises an excipient or a carrier that optimizes the seeding of
the transferred microbiota.
[0015] In one embodiment of any of the above methods of the
invention, the vaginal microbiota inoculum is delivered using an
absorbent material or device (e.g., gauze, sponge, or tampon). In
one specific embodiment, the vaginal microbiota inoculum is
transferred to said absorbent material or device by introducing
said absorbent material or device (e.g., for at least 5 minutes) in
vagina prior to the birth or at the time of Cesarean section.
[0016] In one embodiment of any of the above methods, the vaginal
microbiota inoculum, after it is obtained from the subject's mother
or the donor, is stored in a frozen form.
[0017] In one embodiment of any of the above methods, the vaginal
microbiota inoculum, after it is obtained from the subject's mother
or the donor, is processed to isolate desired bacteria as single or
mixed cultures and such mixed or single cultures are then
administered to the infant.
[0018] In one embodiment of any of the above methods, the vaginal
microbiota inoculum is lyophilized after it is obtained from the
subject's mother or the donor and reconstituted prior to the
administration to the infant.
[0019] In one embodiment of any of the above methods, prior to
obtaining vaginal microbiota from the newborn's mother or the
donor, it is verified that said mother or donor does not have Group
B Streptococcus (GBS) and/or sexually transmitted diseases such as,
e.g., human immunodeficiency virus (HIV) and/or Chlamydia. In one
embodiment of any of the above methods, prior to obtaining vaginal
microbiota from the newborn's mother or the donor, it is verified
that said mother's or donor's vaginal pH is less than 4.5.
[0020] In one embodiment of any of the above methods of the
invention, the newborn's mother or the donor has not been
administered antibiotic compounds within a certain period prior to
the collection of the microbiota (preferably, for at least one
month prior to the collection of the microbiota), is not obese or
overweight (preferably has body mass index (BMI) scores of below
25, most preferably between 18.5 and 24.9), and does not have
irritable bowel disease, Crohn's disease, ulcerative colitis,
irritable bowel syndrome, celiac disease, colorectal cancer, and a
family history of these diseases.
[0021] In one embodiment of any of the above methods, the method
further comprises monitoring the infant's microbiota after the
administration of the vaginal microbiota by: (a) determining a
relative abundance of one or more bacterial taxa in a microbiota
sample obtained from the infant (e.g., isolated from feces, skin,
oral mucosa, conjunctive mucosa, or nasal mucosa), and (b)
comparing the relative abundance(s) determined in step (a) to (i) a
predetermined standard value or (ii) to the abundance(s) of the
same taxa in a control subject (e.g., a vaginally delivered
full-term healthy infant) or (iii) to the average value of
abundances of the same taxa in several control subjects.
Non-limiting examples of the methods which can be used for
determining the relative abundance of the bacterial taxa include,
e.g., quantitative polymerase chain reaction (qPCR), sequencing of
bacterial 16S rRNA, shotgun metagenome sequencing, and
metabolomics. In one specific embodiment, the method involves
determining a relative abundance of one or more bacteria from the
taxa selected from the group consisting of Lactobacillus,
Bacteriodales, Bacteroides, Parabacteroides, Bacteroidacea,
Porphyromonadaceae, Coriobacteriales, Bifidobacterium,
Clostridiaceae, Stenotrophomonas, and Gemella. In one specific
embodiment, the method involves determining a relative abundance of
one or more bacteria from the taxa recited in Table 1A. In one
specific embodiment, the method involves determining a relative
abundance of bacterial species recited in Table 1B. In one specific
embodiment, the method involves determining a relative abundance of
one or more bacteria from the family Neisseriaceae.
[0022] In a separate aspect, the invention provides a method for
restoring normal microbiota in an infant delivered by Cesarean
section, said method comprising administering to said infant at the
time of birth and/or within the first 4 months of life an effective
amount of a probiotic composition, wherein said probiotic
composition (i) stimulates growth and/or activity of bacteria which
are under-represented in microbiota of said infant as compared to
vaginally delivered full-term infants, and/or (ii) inhibits growth
and/or activity of bacteria which are over-represented in
microbiota of said infant as compared to vaginally delivered
full-term infants.
[0023] In a related aspect, the invention provides a method for
restoring normal microbiota in a pre-term infant, said method
comprising administering to said infant at the time of birth and/or
within the first 4 months of life an effective amount of a
probiotic composition, wherein said probiotic composition (i)
stimulates growth and/or activity of bacteria which are
under-represented in microbiota of said infant as compared to
vaginally delivered full-term infants, and/or (ii) inhibits growth
and/or activity of bacteria which are over-represented in
microbiota of said infant as compared to vaginally delivered
full-term infants.
[0024] In another aspect, the invention provides a method for
treating (e.g., preventing or ameliorating) a disease in a subject
associated with the subject's delivery by Cesarean section or with
the subject's pre-term birth, said method comprising administering
to said subject at the time of birth and/or within the first 4
months of life a therapeutically effective amount of a probiotic
composition, wherein said probiotic composition (i) stimulates
growth and/or activity of bacteria which are under-represented in
microbiota of said infant as compared to vaginally delivered
full-term infants, and/or (ii) inhibits growth and/or activity of
bacteria which are over-represented in microbiota of said infant as
compared to vaginally delivered full-term infants. In one
embodiment, said disease is an inflammatory or an autoimmune
disorder. In one embodiment, said disease is selected from the
group consisting of autoimmune diseases, allergic diseases,
infectious diseases, and rejection in organ transplantations. In
one embodiment, said disease is selected from the group consisting
of asthma, allergy, celiac disease, type 1 diabetes, obesity,
necrotizing enterocolitis, inflammatory bowel disease (IBD),
ulcerative colitis, Crohn's disease, sprue, autoimmune arthritis,
rheumatoid arthritis, multiple sclerosis, graft vs. host disease
following bone marrow transplantation, osteoarthritis, juvenile
chronic arthritis, Lyme arthritis, psoriatic arthritis, reactive
arthritis, spondyloarthropathy, systemic lupus erythematosus,
insulin dependent diabetes mellitus, thyroiditis, asthma,
psoriasis, dermatitis scleroderma, atopic dermatitis, graft versus
host disease, acute or chronic immune disease associated with organ
transplantation, sarcoidosis, and atherosclerosis.
[0025] In one embodiment of any of the above methods involving
administration of a probiotic composition, said probiotic
composition comprises one or more bacterial strains from one or
more taxa selected from the group consisting of Lactobacillus,
Bacteriodales, Bacteroides, Parabacteroides, Bacteroidacea,
Porphyromonadaceae, Coriobacteriales Bifidobacterium,
Clostridiaceae, Stenotrophomonas, and Gemella. In one embodiment of
any of the above methods involving administration of a probiotic
composition, said probiotic composition comprises one or more
bacterial strains from one or more taxa recited in Table 1A. In one
embodiment of any of the above methods involving administration of
a probiotic composition, said probiotic composition comprises one
or more bacterial strains from one or more species recited in Table
1B. In one embodiment of any of the above methods involving
administration of a probiotic composition, said probiotic
composition comprises one or more OTUs which are independently
characterized by, i.e., at least 95%, 96%, 97%, 98%, 99% or
including 100% sequence identity to sequences listed in SEQ ID NOS
1-12 or 16S rRNA sequences of the bacterial species recited in
Table 4 or Table 1B. In another embodiment, the OTUs may be
characterized by one or more of the variable regions of the 16S
rRNA sequence (V1-V9). These regions in bacteria are defined by
nucleotides 69-99, 137-242, 433-497, 576-682, 822-879, 986-1043,
1117-1173, 1243-1294 and 1435-1465 respectively using numbering
based on the E. coli system of nomenclature. (See, e.g., Brosius et
al., Complete nucleotide sequence of a 16S ribosomal RNA gene from
Escherichia coli, PNAS 75(10):4801-4805 (1978)). In some
embodiments, at least one of the V1, V2, V3, V4, V5, V6, V7, V8,
and V9 regions are used to characterize an OTU. In one embodiment,
the V1, V2, and V3 regions are used to characterize an OTU. In
another embodiment, the V3, V4, and V5 regions are used to
characterize an OTU. In another embodiment, the V4 region is used
to characterize an OTU. In one embodiment of any of the above
methods involving administration of a probiotic composition, said
probiotic composition comprises one or more bacterial strains which
are independently characterized by, i.e., at least 95%, 96%, 97%,
98%, or 99% sequence identity to 16S rRNA sequences of the
bacterial species recited in Table 1B or Table 4. In one embodiment
of any of the above methods involving administration of a probiotic
composition, said probiotic composition comprises one or more
bacterial strains from the family Neisseriaceae. In one embodiment
of any of the above methods involving administration of a probiotic
composition, said probiotic composition augments the growth of at
least one type of bacteria not detected in the probiotic or in the
newborn's gastrointestinal (GI) tract, skin, mouth or any body
site, prior to administration. In one embodiment of any of the
above methods involving administration of a probiotic composition,
said probiotic composition comprises one or more bacterial strains
which can be found in a healthy vaginal microbiota from a pregnant
woman in the third trimester of pregnancy before or at the time of
giving birth. In one specific embodiment, said pregnant woman has
not been administered antibiotic compounds within a certain period
prior to the collection of the microbiota (preferably, for at least
one month prior to the collection of the microbiota), is not obese
or overweight (preferably has body mass index (BMI) scores of below
25, most preferably between 18.5 and 24.9), and does not have
irritable bowel disease, Crohn's disease, ulcerative colitis,
irritable bowel syndrome, celiac disease, colorectal cancer, and a
family history of these diseases.
[0026] The probiotic composition useful in any of the above methods
can comprise, without limitation, e.g., live bacterial cells,
conditionally lethal bacterial cells, inactivated bacterial cells,
killed bacterial cells, spores (e.g., germination-competent
spores), recombinant carrier strains, cell extract, and
bacterially-derived products (natural or synthetic
bacterially-derived products such as, e.g., bacterial antigens or
bacterial metabolic products).
[0027] In one embodiment of any of the above methods involving
administration of a probiotic composition, said probiotic
composition comprises (i) a carrier and/or excipient and/or (ii)
one or more prebiotic agents which stimulate growth and/or activity
of one or more bacteria present in the composition. In one specific
embodiment, the probiotic composition comprises an excipient or a
carrier that optimizes the seeding of one or more bacterial strains
contained in said probiotic composition.
[0028] In one embodiment of any of the above methods involving
administration of a probiotic composition, said probiotic
composition is reconstituted from a lyophilized preparation. In one
embodiment of any of the above methods involving administration of
a probiotic composition, said probiotic composition comprises a
buffering agent to adjust pH to the natural vaginal pH at the time
of labor or to a pH of 3.5 to 7.
[0029] In one embodiment of any of the above methods involving
administration of a probiotic composition, the probiotic
composition is delivered to the mouth, nose, and/or skin of the
infant and/or by placing it on the maternal breast and/or chest. In
one embodiment, the probiotic composition is administered to the
infant by a route selected from the group consisting of oral,
topical, rectal (e.g., by enema), mucosal, sublingual, nasal, and
via naso/oro-gastric gavage. In one embodiment, the probiotic
composition is delivered to the infant in a form of a liquid, foam,
cream, spray, powder, or gel. In one embodiment, the probiotic
composition is delivered using an absorbent material or device
(e.g., gauze, sponge, tampon, or other applicators). In one
embodiment, the probiotic composition comprises a buffering agent
(e.g., sodium bicarbonate, infant formula or sterilized human
milk).
[0030] In one embodiment of any of the above methods involving
administration of a probiotic composition, the probiotic
composition is administered conjointly with a prebiotic which
stimulates growth and/or activity of bacteria contained in the
probiotic composition. Non-limiting examples of useful prebiotics
include, e.g., fructooligosaccharides (FOS),
galactooligosaccharides (GOS), human milk oligosaccharides (HMO),
Lacto-N-neotetraose, D-Tagatose, xylo-oligosaccharides (XOS),
arabinoxylan-oligosaccharides (AXOS), N-acetylglucosamine,
N-acetylgalactosamine, glucose, arabinose, maltose, lactose,
sucrose, cellobiose, amino acids, alcohols, resistant starch (RS),
and any mixtures thereof. In one specific embodiment, the prebiotic
is derived from microorganisms that show stimulation by human milk
components. In one specific embodiment, the probiotic and prebiotic
are administered in one composition, or simultaneously as two
separate compositions, or sequentially.
[0031] In a separate embodiment, the invention provides a method
for diagnosing abnormal microbiota development in an infant,
comprising: (a) determining a relative abundance of one or more
bacterial taxa in a microbiota sample obtained from the infant, and
(b) comparing the relative abundance(s) determined in step (a) to
(i) a predetermined standard value or (ii) to the abundance(s) of
the same taxa in a control subject or (iii) to the median value of
abundances of the same taxa in several control subjects, wherein
the control subject is a vaginally delivered full-term healthy
infant. Non-limiting examples of the methods which can be used for
determining the relative abundance of the bacterial taxa include,
e.g., quantitative polymerase chain reaction (qPCR), sequencing of
bacterial 16S rRNA, shotgun metagenome sequencing, and
metabolomics. In one embodiment, the diagnostic method involves
determining a relative abundance of one or more bacteria from one
or more taxa selected from the group consisting of Lactobacillus,
Bacteriodales (e.g., S24-7), Bacteroides, Parabacteroides,
Bacteroidacea, Porphyromonadaceae, Coriobacteriales
Bifidobacterium, Clostridiaceae, Stenotrophomonas, and Gemella. In
one embodiment, the diagnostic method involves determining a
relative abundance of one or more bacteria from one or more taxa
present in a healthy vaginal microbiota from a pregnant woman in
the third trimester of pregnancy before or at the time of giving
birth. In one embodiment, the diagnostic method involves
determining a relative abundance of one or more bacteria from one
or more taxa recited in Table 1A. In one embodiment, the diagnostic
method involves determining a relative abundance of one or more
bacteria from one or more species recited in Table 1B. In one
embodiment, the diagnostic method involves determining a relative
abundance of one or more bacteria from the family
Neisseriaceae.
[0032] In one embodiment of any of the above methods, the infant
(or subject) is human. In one embodiment of any of the above
methods, the infant is a newborn.
[0033] In another aspect, the invention provides a composition
comprising (i) a vaginal microbiota inoculum and (ii) a carrier
and/or excipient and/or one or more prebiotic agents which
stimulate growth and/or activity of one or more bacteria present in
the inoculum.
[0034] In a further aspect, the invention provides a probiotic
composition comprising (a) one or more bacterial strains and (b) a
carrier and/or excipient and/or one or more prebiotic agents which
stimulate growth and/or activity of one or more of said bacterial
strains, wherein said probiotic composition (i) stimulates growth
and/or activity of bacteria which are under-represented in
microbiota of an infant delivered by Cesarean section or born
prematurely as compared to vaginally delivered full-term healthy
infants, and/or (ii) inhibits growth and/or activity of bacteria
which are over-represented in microbiota of said infant as compared
to vaginally delivered full-term healthy infants. In one
embodiment, the composition comprises two or more different
bacterial strains.
[0035] Non-limiting examples of bacteria which can be present in
any of the compositions of the invention comprise
(i) bacteria from one or more taxa selected from the group
consisting of Lactobacillus, Bacteriodales (e.g., S24-7),
Bacteroides, Parabacteroides, Bacteroidacea, Porphyromonadaceae,
Coriobacteriales, Bifidobacterium, Clostridiaceae,
Stenotrophomonas, and Gemella; (ii) bacteria from one or more taxa
recited in Table 1A; (iii) bacteria from one or more species
recited in Table 1B; (iv) bacteria from family Neisseriaceae.
[0036] In one embodiment of any of the compositions of the
invention, the composition comprises one or more OTUs which are
independently characterized by, i.e., at least 95%, 96%, 97%, 98%,
99% or including 100% sequence identity to sequences listed in SEQ
ID NOS 1-12 or 16S rRNA sequences of the bacterial species recited
in Table 4 or Table 1B. In another embodiment, the OTUs may be
characterized by one or more of the variable regions of the 16S
rRNA sequence (V1-V9). These regions in bacteria are defined by
nucleotides 69-99, 137-242, 433-497, 576-682, 822-879, 986-1043,
1117-1173, 1243-1294 and 1435-1465 respectively using numbering
based on the E. coli system of nomenclature. (See, e.g., Brosius et
al., Complete nucleotide sequence of a 16S ribosomal RNA gene from
Escherichia coli, PNAS 75(10):4801-4805 (1978)). In some
embodiments, at least one of the V1, V2, V3, V4, V5, V6, V7, V8,
and V9 regions are used to characterize an OTU. In one embodiment,
the V1, V2, and V3 regions are used to characterize an OTU. In
another embodiment, the V3, V4, and V5 regions are used to
characterize an OTU. In another embodiment, the V4 region is used
to characterize an OTU. In one embodiment of any of the
compositions of the invention, the composition comprises one or
more bacterial strains which are independently characterized by,
i.e., at least 95%, 96%, 97%, 98%, or 99% sequence identity to 16S
rRNA sequences of the bacterial species recited in Table 1B or
Table 4. In one embodiment of any of the compositions of the
invention, the composition augments the growth of at least one type
of bacteria not detected in the probiotic or in the newborn's
gastrointestinal (GI) tract, skin, mouth, or any body site, prior
to administration.
[0037] In one embodiment of any of the compositions of the
invention, said composition comprises one or more bacterial strains
which can be found in a healthy vaginal microbiota from a pregnant
woman in the third trimester of pregnancy before or at the time of
giving birth. In one specific embodiment, the woman has not been
administered antibiotic compounds within a certain period prior to
isolation of bacteria (preferably, for at least one month prior to
isolation of bacteria), has body mass index (BMI) between 18.5 and
24.9, does not have Group B Streptococcus (GBS), human
immunodeficiency virus (HIV), Chlamydia, and/or sexually
transmitted diseases, has vaginal pH less than 4.5, and does not
have irritable bowel disease, Crohn's disease, ulcerative colitis,
irritable bowel syndrome, celiac disease, colorectal cancer or a
family history of these diseases.
[0038] In one embodiment of any of the compositions of the
invention, the composition comprises a buffering agent to adjust pH
to the natural vaginal pH at the time of labor or to a pH of 3.5 to
7. In one embodiment of any of the compositions of the invention,
the composition comprises an excipient or a carrier that optimizes
the seeding of one or more bacterial strains contained in the
composition. In one embodiment of any of the compositions of the
invention, the composition is formulated for storage in a frozen
form. In one embodiment of any of the compositions of the
invention, said composition is a lyophilized composition. Any of
the compositions of the invention can contain, e.g., live bacterial
cells, conditionally lethal bacterial cells, inactivated bacterial
cells, killed bacterial cells, spores (e.g., germination-competent
spores), recombinant carrier strains, cell extract, or
bacterially-derived products (natural or synthetic
bacterially-derived products such as, e.g., bacterial antigens or
metabolic products). In one embodiment of any of the compositions
of the invention, the composition is formulated for delivery to the
mouth, nose, and/or skin of the infant and/or for placing it on the
maternal breast and/or chest. In one embodiment of any of the
compositions of the invention, the composition is formulated for
delivery by a route selected from the group consisting of oral,
topical, rectal, mucosal, sublingual, nasal, and via
naso/oro-gastric gavage. In one embodiment of any of the
compositions of the invention, the composition is in a form of a
liquid, foam, cream, spray, powder, or gel. In one embodiment of
any of the compositions of the invention, the composition comprises
a buffering agent (e.g., sodium bicarbonate, infant formula or
sterilized human milk). In one embodiment of any of the
compositions of the invention, the composition comprises a
prebiotic which stimulates growth and/or activity of one or more
bacteria contained in the composition. Non-limiting examples of
useful prebiotics include, e.g., fructooligosaccharides (FOS),
galactooligosaccharides (GOS), human milk oligosaccharides (HMO),
Lacto-N-neotetraose, D-Tagatose, xylo-oligosaccharides (XOS),
arabinoxylan-oligosaccharides (AXOS), N-acetylglucosamine,
N-acetylgalactosamine, glucose, arabinose, maltose, lactose,
sucrose, cellobiose, amino acids, alcohols, resistant starch (RS),
and any mixtures thereof.
[0039] In a related aspect, the invention provides an absorbent
material or device (e.g., gauze, sponge, or tampon) comprising any
of the compositions of the invention.
[0040] In another related aspect, the invention provides a method
for restoring normal microbiota in an infant delivered by Cesarean
section or a method for restoring normal microbiota in a pre-term
infant, said method comprising administering to said infant at the
time of birth and/or within the first 4 months of life an effective
amount of any of the compositions of the invention.
[0041] In another related aspect, the invention provides a method
for treating a disease in a subject associated with the subject's
delivery by Cesarean section or with the subject's pre-term birth,
said method comprising administering to said subject at the time of
birth and/or within the first 4 months of life a therapeutically
effective amount of any of the compositions of the invention.
[0042] It is also contemplated that when used to treat various
diseases, the compositions and methods of the present invention can
be utilized in combination with other therapeutic methods/agents
suitable for the same or similar diseases. Such other therapeutic
methods/agents can be co-administered (simultaneously or
sequentially) to generate additive or synergistic effects. Suitable
effective dosages for each agent may be lowered due to the additive
action or synergy.
[0043] In one embodiment of any of the above methods, the infant
(or subject) is human. In one embodiment of any of the above
methods, the infant is a newborn.
[0044] These and other aspects of the present invention will be
apparent to those of ordinary skill in the art in the following
description, claims and drawings.
BRIEF DESCRIPTION OF THE DRAWINGS
[0045] The patent or application file contains at least one drawing
executed in color. Copies of this patent or patent application
publication with color drawing(s) will be provided by the Office
upon request and payment of the necessary fee.
[0046] FIG. 1. Restoring the maternal microbiota in C-section born
infants. When antibiotics are administered 1 hour prior to the
C-section procedure, a gauze is inserted in the mothers' vagina,
and extracted when the procedure starts. The gauze, kept in a
sterile container, is used to swab the newborn as soon as possible
after birth, starting with the mouth, face and rest of the
body.
[0047] FIG. 2. Mean relative abundance of predominant bacteria
(>1% in any sample) in mothers and babies of each delivery
group, during the first month of life of the baby. Taxa are
reported at the lowest identifiable level.
[0048] FIGS. 3(a)-3(c). Alpha diversity of baby oral (a), anal (b)
and skin (forehead, arm and foot; c) samples, in relation to
maternal sites, during the first 30 days of life of the baby. At
birth, the bacterial diversity in baby's mouth and anus (but not in
the skin) is higher than the maternal vagina diversity (green
area), but during the first week, it decreases to values below or
similar to vaginal diversity, remaining low during the period of
strict lactation (about 3 months).
[0049] FIG. 4. PCoA of the infant anal and skin microbiota during
the first month of life, in relation to maternal sites. The anal
microbiota from C-section-inoculated newborns cluster close to that
in vaginally delivered babies at day 1. Non inoculated C-section
babies cluster separately until the first week of life.
[0050] FIG. 5. Lefse analyses depicting overrepresented taxa in the
skin forehead of infants by mode of delivery at different times
after birth.
DETAILED DESCRIPTION
[0051] The present invention provides methods for restoring
bioactivity and diversity of normal microbiota in pre-term newborns
and/or newborns delivered by Cesarean section and methods for
treating (e.g., preventing or ameliorating) diseases associated
with delivery by Cesarean section or pre-term birth comprising
administering to said newborns at the time of birth or shortly
thereafter an effective amount of a vaginal microbiota inoculum
obtained from the newborn's mother or a donor during the third
trimester of pregnancy before or at the time of giving birth or an
effective amount of a probiotic composition, wherein said probiotic
composition (i) stimulates growth and/or activity of bacteria which
are under-represented in microbiota of said newborn as compared to
vaginally delivered full-term newborns, and/or (ii) inhibits growth
and/or activity of bacteria which are over-represented in
microbiota of said newborn as compared to vaginally delivered
full-term newborns. Also provided are methods for diagnosing
abnormal microbiota development in a newborn, comprising
determining a relative abundance of one or more bacterial taxa in a
microbiota sample obtained from said newborn.
DEFINITIONS
[0052] As used herein, the terms "microbe" or "microorganism"
encompass both prokaryotic organisms including bacteria and
archaea, and eukaryotic organisms, including fungi, present in
mammalian microbiota.
[0053] The terms "vaginal microbiota" or "vaginal flora" or
"vaginal microbiome" are used interchangeably and refer to the
microorganisms that colonize the vagina.
[0054] The term "restoring normal microbiota" is used herein to
refer to restoring microbiota of an infant (e.g., skin, oral,
nasal, gastrointestinal, or any other mucosal microbiota) to the
level of bioactivity and diversity of corresponding microbiota of a
healthy infant delivered naturally, i.e., through labor and vaginal
exposure. This may also be considered as normalizing the
microbiota, populating the microbiota, populating normal
microbiota, preventing the onset of dysbiosis, or augmenting the
growth of at least one type of bacteria in an infant. Preferably,
such healthy naturally delivered "control" infant was born to a
mother who has not been administered antibiotic compounds within a
certain period prior to the delivery (preferably, for at least one
month prior to the delivery), is not obese or overweight
(preferably has body mass index (BMI) scores of below 25, most
preferably between 18.5 and 24.9), does not have Group B
Streptococcus (GBS), human immunodeficiency virus (HIV), Chlamydia,
and/or sexually transmitted diseases, has vaginal pH less than 4.5,
and does not have irritable bowel disease, Crohn's disease,
ulcerative colitis, irritable bowel syndrome, celiac disease,
colorectal cancer and a family history of these diseases.
[0055] Specific taxa and changes in microbiota discussed herein can
be detected using various methods, including without limitation
quantitative PCR (qPCR) or high-throughput sequencing (e.g.,
shotgun metagenome sequencing) methods which detect over- and
under-represented genes in the total bacterial population (e.g.,
454-sequencing for community analysis; screening of microbial 16S
ribosomal RNAs (16S rRNA), etc.), or transcriptomic or proteomic
studies that identify lost or gained microbial transcripts or
proteins within total bacterial populations, or metabolomics. See,
e.g., U.S. Patent Publication No. 2010/0074872; Eckburg et al.,
Science, 2005, 308:1635-8; Costello et al., Science, 2009,
326:1694-7; Grice et al., Science, 2009, 324:1190-2; Li et al.,
Nature, 2010, 464: 59-65; Bjursell et al., Journal of Biological
Chemistry, 2006, 281:36269-36279; Mahowald et al., PNAS, 2009,
14:5859-5864; Wikoff et al., PNAS, 2009, 10:3698-3703.
[0056] As used herein, the term "16S rRNA sequencing" refers to the
sequencing of 16S ribosomal RNA (rRNA) gene sequences by using
primers such as universal primers and/or species-specific primers
to identify the bacteria present in a sample. 16S rRNA genes
contain both highly conserved sites and hypervariable regions that
can provide species-specific signature sequences useful for
identification of bacteria. Such universal primers are well known
in the art.
[0057] As used herein, the term "operational taxonomic unit" or
"OTU" refers to group of bacterial sequences that differ among each
other in <97% identity. A "type" or a plurality of "types" of
bacteria includes an OTU or a plurality of different OTUs, and also
encompasses differences in species, genus, family or order of
bacteria. The specific genetic sequence may be the 16S rRNA
sequence or a portion of the 16S rRNA sequence or it may be a
functionally conserved housekeeping gene found broadly across the
eubacterial kingdom.
[0058] As used herein, the term "pre-term" as in pre-term
newborn/infant or pre-term birth refers to any pre-term birth,
including delivery before the 37-week gestation period. In some
embodiments, pre-term includes any birth on or before about 37
weeks. In some embodiments, delivery is from about 37 weeks to 39
weeks. In some embodiments, delivery is from about 32 weeks to 37
weeks. In some embodiments, delivery is from about 32 weeks to 28
weeks. In some embodiments, delivery is from about 23 weeks to 28
weeks. References to weeks of gestation include part weeks, such
that a reference to 32 weeks includes both 32 weeks and 0 days
through 32 weeks and 6 days.
[0059] As used herein, the term "probiotic" refers to a
substantially pure bacteria (i.e., a single isolate, of, e.g., live
bacterial cells, conditionally lethal bacterial cells, inactivated
bacterial cells, killed bacterial cells, spores, recombinant
carrier strains), or a mixture of desired bacteria, bacteria
components or bacterial extract, or bacterially-derived products
(natural or synthetic bacterially-derived products such as, e.g.,
bacterial antigens or metabolic products) and may also include any
additional components that can be administered to a mammal. Such
compositions are also referred to herein as a "bacterial
inoculant."
[0060] As used herein, the term "prebiotic" refers to an agent that
increases the number and/or activity of one or more desired
bacteria, enhancing their growth. Non-limiting examples of
prebiotics useful in the methods of the present invention include
fructooligosaccharides (e.g., oligofructose, inulin, inulin-type
fructans), galactooligosaccharides, human milk oligosaccharides
(HMO), Lacto-N-neotetraose, D-Tagatose, xylo-oligosaccharides
(XOS), arabinoxylan-oligosaccharides (AXOS), N-acetylglucosamine,
N-acetylgalactosamine, glucose, other five- and six-carbon sugars
(such as arabinose, maltose, lactose, sucrose, cellobiose, etc.),
amino acids, alcohols, resistant starch (RS), and mixtures thereof.
See, e.g., Ramirez-Farias et al., Br J Nutr (2008) 4:1-10;
Pool-Zobel and Sauer, J Nutr (2007), 137:2580S-2584S.
[0061] The terms "treat" or "treatment" of a state, disorder or
condition include: (1) preventing, delaying, or reducing the
incidence and/or likelihood of the appearance of at least one
clinical or sub-clinical symptom of the state, disorder or
condition developing in a subject that may be afflicted with or
predisposed to the state, disorder or condition but does not yet
experience or display clinical or subclinical symptoms of the
state, disorder or condition; or (2) inhibiting the state, disorder
or condition, i.e., arresting, reducing or delaying the development
of the disease or a relapse thereof (in case of maintenance
treatment) or at least one clinical or sub-clinical symptom
thereof; or (3) relieving the disease, i.e., causing regression of
the state, disorder or condition or at least one of its clinical or
sub-clinical symptoms. The benefit to a subject to be treated is
either statistically significant or at least perceptible to the
patient or to the physician.
[0062] As used herein, the term "therapeutically effective amount"
refers to the amount of a microbiota inoculum or probiotic that,
when administered to a subject for treating (e.g., preventing or
ameliorating) a state, disorder or condition, is sufficient to
effect such treatment. The "therapeutically effective amount" will
vary depending, e.g., on the bacteria or analogues administered as
well as the disease and physical conditions and responsiveness of
the subject to be treated.
[0063] As used herein, the phrase "pharmaceutically acceptable"
refers to molecular entities and compositions that are generally
regarded as physiologically tolerable.
[0064] As used herein, the term "combination" of a microbiota
inoculum or probiotic and at least a second pharmaceutically active
ingredient means at least two, but any desired combination of
compounds can be delivered simultaneously or sequentially (e.g.,
within a 24 hour period).
[0065] The terms "patient", "individual", "subject", and "animal"
are used interchangeably herein and refer to mammals, including,
without limitation, human and veterinary animals (e.g., cats, dogs,
cows, horses, sheep, pigs, etc.) and experimental animal models. In
a preferred embodiment, the subject (e.g., infant) is a human.
[0066] As used herein, the term "infant" refers to subjects from
birth until the age when microbiome development is completed and
encompasses newborn subjects. For humans, "infant" refers to
subjects from birth to 3 years of age. In some embodiments, an
infant treated using any of the methods or compositions of the
invention is treated during the stage of development relevant (or
critical) to microbiome development.
[0067] As used herein, the term "stimulate" when used in connection
with growth and/or activity of bacteria encompasses the term
"enhance".
[0068] The term "carrier" refers to a diluent, adjuvant, excipient,
or vehicle with which the compound is administered. Such
pharmaceutical carriers can be sterile liquids, such as water and
oils, including those of petroleum, animal, vegetable or synthetic
origin, such as peanut oil, soybean oil, mineral oil, sesame oil
and the like. Water or aqueous solution saline solutions and
aqueous dextrose and glycerol solutions are preferably employed as
carriers, particularly for injectable solutions. Alternatively, the
carrier can be a solid dosage form carrier, including but not
limited to one or more of a binder (for compressed pills), a
glidant, an encapsulating agent, a flavorant, and a colorant.
Suitable pharmaceutical carriers are described in "Remington's
Pharmaceutical Sciences" by E. W. Martin.
[0069] The term "about" or "approximately" means within a
statistically meaningful range of a value. Such a range can be
within an order of magnitude, preferably within 50%, more
preferably within 20%, still more preferably within 10%, and even
more preferably within 5% of a given value or range. The allowable
variation encompassed by the term "about" or "approximately"
depends on the particular system under study, and can be readily
appreciated by one of ordinary skill in the art.
[0070] The terms "a," "an," and "the" do not denote a limitation of
quantity, but rather denote the presence of "at least one" of the
referenced item.
[0071] The practice of the present invention employs, unless
otherwise indicated, conventional techniques of statistical
analysis, molecular biology (including recombinant techniques),
microbiology, cell biology, and biochemistry, which are within the
skill of the art. Such tools and techniques are described in detail
in e.g., Sambrook et al. (2001) Molecular Cloning: A Laboratory
Manual. 3rd ed. Cold Spring Harbor Laboratory Press: Cold Spring
Harbor, N.Y.; Ausubel et al. eds. (2005) Current Protocols in
Molecular Biology. John Wiley and Sons, Inc.: Hoboken, N.J.;
Bonifacino et al. eds. (2005) Current Protocols in Cell Biology.
John Wiley and Sons, Inc.: Hoboken, N.J.; Coligan et al. eds.
(2005) Current Protocols in Immunology, John Wiley and Sons, Inc.:
Hoboken, N.J.; Coico et al. eds. (2005) Current Protocols in
Microbiology, John Wiley and Sons, Inc.: Hoboken, N.J.; Coligan et
al. eds. (2005) Current Protocols in Protein Science, John Wiley
and Sons, Inc.: Hoboken, N.J.; and Enna et al. eds. (2005) Current
Protocols in Pharmacology, John Wiley and Sons, Inc.: Hoboken, N.J.
Additional techniques are explained, e.g., in U.S. Pat. No.
7,912,698 and U.S. Patent Appl. Pub. Nos. 2011/0202322 and
2011/0307437.
Methods and Compositions of the Invention
[0072] The vertical transmission of microbiota from mother to child
during labor and birth is highly conserved in mammals, suggesting
evolutionary fitness (35). The present invention provides that
major microbiota deficiencies at birth in pre-term newborns or
newborns delivered by Cesarean section can be restored by the
exposure to maternal (or third trimester donor) vaginal microbiota
or probiotics derived therefrom.
[0073] Microbiota donor subjects are generally of good health and
have microbiota consistent with such good health. Often, the donor
subjects have not been administered antibiotic compounds within a
certain period prior to the collection of the microbiota
(preferably, for at least one month prior to the collection of the
microbiota). In certain embodiments, the donor subjects are not
obese or overweight, and may have body mass index (BMI) scores of
below 25, such as between 18.5 and 24.9. In other embodiments, the
donor subjects do not have irritable bowel disease, Crohn's
disease, ulcerative coliti), irritable bowel syndrome, celiac
disease, colorectal cancer and a family history of these diseases.
In other embodiments, donors have been screened for pathogens using
standard techniques known to one in the art (e.g. nucleic acid
testing, serological testing, antigen testing, culturing
techniques, enzymatic assays, assays of cell free fecal filtrates
looking for toxins on susceptible cell culture substrates).
[0074] In some embodiments, donors are also selected for the
presence of certain genera and/or species that provide increased
efficacy of therapeutic compositions containing these genera or
species. In other embodiments, donors are preferred that produce
relatively higher concentrations of spores than other donors. In
further embodiments, donors are preferred that provide spores
having increased efficacy; this increased efficacy can be measured
using in vitro or animal studies. In some embodiments, the donor
may be subjected to one or more pre-donation treatments in order to
reduce undesired material in the collected microbiota, and/or
increase desired spore populations.
[0075] It is advantageous to screen the health of the donor subject
prior to and optionally, one or more times after, the collection of
the microbiota material. Such screening identifies donors carrying
pathogenic materials such as viruses (e.g., HIV, hepatitis, polio)
and pathogenic bacteria. Post-collection, donors are screened about
one week, two weeks, three weeks, one month, two months, three
months, six months, one year or more than one year, and the
frequency of such screening may be daily, weekly, bi-weekly,
monthly, bi-monthly, semi-yearly or yearly. Donors that are
screened and do not test positive, either before or after donation
or both, are considered "validated" donors.
[0076] Methods for collection and preparation of vaginal microbiota
are well known in the art. The vaginal microbiota can be stored,
e.g., as frozen or lyophilized preparations (said lyophilized
preparations can be reconstituted prior to the administration to
the infant) or can be processed to isolate desired bacteria as
single or mixed cultures and then stored. Vaginal microbiota and
probiotics can be administered in various forms, including but not
limited to, solid (e.g., powder), liquid, gel, cream, spray, foam,
etc. The invention contemplates the use of various carriers,
containers, and devices suitable for holding the vaginal microbiota
in a suitable condition. For vaginal microbiota and live bacteria
probiotic preparations, the carrier should preferably contain an
ingredient that promotes viability of the bacteria during storage.
The formulations can include added ingredients to improve
palatability, improve shelf-life, impart nutritional benefits, and
the like. In certain embodiments, the microbiota and probiotic
preparations used in the methods of the invention comprise a
buffering agent to adjust pH to the natural vaginal pH at the time
of labor (pH of 3.5-7) or to a pH (3.5-7) that optimizes the
seeding of the transferred microbiota.
[0077] The invention also contemplates in a broad scope any means
for transferring, including but not limited to various absorbent
materials (e.g., in the form of gauze, sponge, tampon, etc.),
and/or needle, tube, catheter, etc. The vaginal microbiota can be
transferred to absorbent material or device, e.g., by introducing
said absorbent material or device in vagina prior to the birth or
at the time of Cesarean section (e.g., for at least 5 minutes).
[0078] The invention provides that the collected vaginal microbiota
or probiotics can be administered to any body part colonized in the
newborns, including but not limited to, mouth, nasal mucosa, skin,
etc. Alternatively (or in addition), vaginal microbiota or
probiotics can be placed on the maternal breast and/or chest.
Non-limiting examples of suitable routes of administration of
vaginal microbiota and probiotics include oral (e.g., swabbing or
via feeding tube or baby bottle), topical, rectal (e.g., by enema),
mucosal, sublingual, nasal, and via naso/oro-gastric gavage. If a
reproducible and measured dose is desired, the bacteria can be
administered by a rumen cannula.
[0079] The dosages of the microbiota inoculum or probiotic
administered in the methods of the invention will vary widely,
depending upon the newborn's physical parameters, the frequency of
administration, the manner of administration, the clearance rate,
and the like. The initial dose may be larger, and might be followed
by smaller maintenance doses. The dose may be administered as
infrequently as weekly or biweekly, or fractionated into smaller
doses and administered daily, semi-weekly, etc., to maintain an
effective dosage level. It is contemplated that a variety of doses
will be effective to achieve colonization, e.g. 10.sup.6, 10.sup.7,
10.sup.8, 10.sup.9, and 10.sup.10 CFU for example, can be
administered in a single dose. Lower doses can also be effective,
e.g., 10.sup.4, and 10.sup.5 CFU.
[0080] Bacterial strains administered in probiotics according to
the methods of the present invention can comprise live bacteria.
One or several different bacterial inoculants can be administered
simultaneously or sequentially (including administering at
different times). Such bacteria can be isolated from vaginal
microbiota and grown in culture using known techniques. However,
many bacterial species are very difficult to culture and
administration of others may lead to various undesirable
side-effects. The present invention also comprises administering
"bacterial analogues", such as recombinant carrier strains
expressing one or more heterologous genes derived from the relevant
bacterial species. The use of such recombinant bacteria may allow
the use of lower therapeutic amounts due to higher protein
expression. In certain embodiments, spores, killed bacterial cells
and bacterial cell extracts can be utilized as the probiotics of
the invention (see, e.g., Round et al., Proc. Natl. Acad. Sci. USA,
2010, 107: 12204). Bacteria in the compositions of the invention
can be from one or more different species and can be, e.g., in the
form of live bacterial cells, conditionally lethal bacterial cells,
inactivated bacterial cells, killed bacterial cells, spores (e.g.,
germination-competent spores), recombinant carrier strains, cell
extract, or bacterially-derived products (natural or synthetic
bacterially-derived products such as, e.g., bacterial antigens or
metabolic products). In one specific embodiment, the composition
comprises at least two different bacterial strains.
[0081] In one specific embodiment, the composition comprises
bacteria from at least two different bacterial species. In some
embodiments, the compositions comprise bacteria from at least 2, 3,
4, 5, 6, 7, 8, 9, 10, 50, 100, 200, 500, or 1000 different
bacterial species.
[0082] In some embodiments, the composition comprises bacteria from
at least one of the taxa provided in Table 1A. In some embodiments,
the composition comprises bacteria from at least 2, 3, 4, 5, 6, 7,
8, 9, 10, 20, or 50 different taxa in Table 1A. In some
embodiments, only nonpathogenic species within the taxa qualify for
use in the compositions or methods herein.
TABLE-US-00001 TABLE 1A Taxa for Inclusion in Compositions and
Methods or for Microbiota Monitoring Family Neisseriacea Genera
Acinetobacter Actinomyces Aerococcus Alloscardovia Anaerococcus
Anaerostipes Anoxybacillus Asticcacaulis Atopobium Bacillus
Bacteroides Bifidobacterium Blastomonas Bradyrhizobium
Brevibacterium Campylobacter Clavibacter Cloacibacterium
Clostridium Comamonas Corynebacterium Dermabacter Devriesea
Dialister Dorea Enterococcus Eremococcus Erysipelatoclostridium
Escherichia Ezakiella Facklamia Fastidiosipila Fenollaria
Finegoldia Fusobacterium Gardnerella Gemella Haemophilus
Helcococcus Herbaspirillum Jonquetella Kocuria Kytococcus
Lactobacillus Lactococcus Leptotrichia Levyella Megasphaera
Methylobacillus Methylobacterium Micrococcus Mobiluncus Mycoplasma
Negativicoccus Novosphingobium Oceanitalea Parabacteroides
Paracoccus Parvimonas Pelistega Peptococcus Peptoniphilus
Peptostreptococcus Polaromonas Porphyromonas Prevotella
Pseudoclavibacter Pseudomonas Rothia Rubrobacter Ruminococcus
Sneathia Sphingobium Sphingopyxis Staphylococcus Stenotrophomonas
Streptococcus Sutterella Ureaplasma Varibaculum Veillonella
Veillonella 1-68 Bacteroidacea Porphyromonadaceae Coriobacteriales
Clostridiaceae Bacteriodales
[0083] In some embodiments, the composition comprises bacteria from
at least one of the species provided in Table 1B. In some
embodiments, the composition comprises bacteria from at least 2, 3,
4, 5, 6, 7, 8, 9, 10, 20, 50, 100, or 150 different bacterial
species in Table 1B. In some embodiments, at least some of the
bacteria chosen from Table 1B are in different genera, including,
but not limited to 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, or 50 different
genera. In other embodiments, at least some of the bacteria chosen
from Table 1B are in the same genera.
TABLE-US-00002 TABLE 1B Species for Inclusion in Compositions and
Methods or for Microbiota Monitoring Acinetobacter baumannii
Acinetobacter gerneri Acinetobacter johnsonii Acinetobacter
radioresistens Acinetobacter schindleri Acinetobacter seifertii
Acinetobacter variabilis Actinomyces europaeus Actinomyces neuii
Aerococcus christensenii Alloscardovia omnicolens Anaerococcus
lactolyticus Anaerococcus murdochii Anaerococcus obesiensis
Anaerococcus octavius Anaerococcus prevotii Anaerococcus
provenciensis Anaerococcus vaginalis Anaerostipes hadrus
Anoxybacillus flavithermus Asticcacaulis excentricus Atopobium
deltae Atopobium vaginae Bacillus vireti Bacteroides finegoldii
Bacteroides vulgatus Bifidobacterium breve, Bifidobacterium
Blastomonas natatoria Bradyrhizobium lupini pseudolongum
Brevibacterium paucivorans Campylobacter coli Campylobacter hominis
Campylobacter ureolyticus Clavibacter michiganensis Cloacibacterium
rupense Clostridium clostridioforme Clostridium perfringens
Comamonas serinivorans Comamonas testosterone Corynebacterium
Corynebacterium appendicis amycolatum Corynebacterium
Corynebacterium Corynebacterium canis argentoratense aurimucosum
Corynebacterium casei Corynebacterium coyleae Corynebacterium
freneyi Corynebacterium imitans Corynebacterium jeikeium
Corynebacterium kroppenstedtii Corynebacterium lactis
Corynebacterium matruchotii Corynebacterium mycetoides
Corynebacterium mycetoides Corynebacterium pilbarense
Corynebacterium pyruviciproducens Corynebacterium Corynebacterium
striatum Corynebacterium spheniscorum terpenotabidum
Corynebacterium thomssenii Corynebacterium Corynebacterium
tuscaniense tuberculostearicum Dermabacter hominis Devriesea
agamarum Dialister micraerophilus Dialister propionicifaciens
Dialister succinatiphilus Dorea longicatena Enterococcus hirae
Eremococcus coleocola Erysipelatoclostridium ramosum Escherichia
marmotae Ezakiella peruensis Facklamia hominis Facklamia ignava
Fastidiosipila sanguinis Fenollaria massiliensis Finegoldia magna
Fusobacterium equinum Fusobacterium nucleatum Fusobacterium
Fusobacterium simiae Gardnerella vaginalis periodonticum Gemella
asaccharolytica, Gemella taiwanensis Haemophilus pittmaniae
Helcococcus sueciensis Herbaspirillum Jonquetella anthropic
chlorophenolicum Kocuria flava strain HO- Kocuria kristinae strain
DSM Kytococcus schroeteri strain 9041 20032 Muenster 2000
Lactobacillus coleohominis Lactobacillus crispatus Lactobacillus
hominis Lactobacillus iners Lactobacillus intestinalis
Lactobacillus jensenii Lactobacillus psittaci Lactobacillus reuteri
Lactobacillus rodentium Lactococcus lactis Levyella massiliensis
Methylobacillus flagellates Methylobacterium aerolatum
Methylobacterium Micrococcus aloeverae strain phyllostachyos AE-6
Mobiluncus curtisii Mycoplasma hominis Negativicoccus
succinicivorans Oceanitalea nanhaiensis Parabacteroides faecis
Parabacteroides merdae Paracoccus communis Parvimonas micra
Pelistega indica Peptococcus niger Peptoniphilus coxii
Peptoniphilus duerdenii Peptoniphilus grossensis Peptoniphilus
koenoeneniae Peptoniphilus lacrimalis Peptoniphilus obesi strain
Peptoniphilus senegalensis Peptoniphilus tyrrelliae ph1
Peptostreptococcus Polaromonas sp Porphyromonas bennonis anaerobius
Porphyromonas somerae Porphyromonas uenonis Prevotella amnii
Prevotella bergensis Prevotella bivia Prevotella buccalis
Prevotella copri Prevotella corporis Prevotella disiens Prevotella
timonensis Pseudoclavibacter bifida Pseudomonas brenneri strain IAM
14848 Pseudomonas helmanticensis Pseudomonas lini Pseudomonas
syringae Rothia amarae strain J18 Rothia mucilaginosa Rubrobacter
calidifluminis Ruminococcus bromii Ruminococcus gnavus Sneathia
sanguinegens Sphingobium yanoikuyae Sphingopyxis Staphylococcus
carnosus macrogoltabida Staphylococcus chromogenes Staphylococcus
petrasii Staphylococcus pseudintermedius Staphylococcus
Stenotrophomonas Streptococcus agalactiae saprophyticus maltophilia
Streptococcus anginosus Streptococcus constellatus Streptococcus
dentisani Streptococcus lactarius Streptococcus thermophiles
Sutterella stercoricanis Ureaplasma urealyticum Varibaculum
cambriense Veillonella dispar Veillonella ratti Bacteriodales
S24-7
[0084] Within a given composition, different bacterial strains can
be contained in equal amounts (even combination) or in various
proportions (uneven combinations) needed for achieving the maximal
biological activity. For example, in a bacterial composition with
two bacterial strains, the strains may be present in from a
1:10,000 ratio to a 1:1 ratio, from a 1:10,000 ratio to a 1:1,000
ratio, from a 1:1,000 ratio to a 1:100 ratio, from a 1:100 ratio to
a 1:50 ratio, from a 1:50 ratio to a 1:20 ratio, from a 1:20 ratio
to a 1:10 ratio, from a 1:10 ratio to a 1:1 ratio. For bacterial
compositions comprising at least three bacterial strains, the ratio
of strains may be chosen pairwise from ratios for bacterial
compositions with two strains. For example, in a bacterial
composition comprising bacterial strains A, B, and C, at least one
of the ratios between strain A and B, the ratio between strain B
and C, and the ratio between strain A and C may be chosen,
independently, from the pairwise combinations above. In one
embodiment, two or more bacterial strains in the composition
produce synergistic activity. In one specific embodiment, the
invention encompasses administering two or more bacteria-containing
compositions to the same subject. Such compositions can be
administered simultaneously or sequentially.
[0085] Spores used in the compositions of the invention can me
isolated, for example, by solvent treatments (e.g., using partially
miscible, fully miscible or an immiscible solvent), chromatographic
treatments (e.g., using hydrophobic interaction chromatography
(HIC) or an affinity chromatography), mechanical treatments (e.g.,
blending, mixing, shaking, vortexing, impact pulverization, and
sonication), filtration treatments, thermal treatments (e.g., 30
seconds in a 100.degree. C. environment followed by 10 minutes in a
50.degree. C.), irradiation treatments (e.g., with ionizing
radiation, typically gamma irradiation, ultraviolet irradiation or
electron beam irradiation provided at an energy level sufficient to
kill pathogenic materials while not substantially damaging the
desired spore populations), centrifugation and density separation
treatments (e.g., using density or mobility gradients or cushions
(e.g., step cushions), such as, e.g., CsCl, Percoll, Ficoll,
Nycodenz, Histodenz or sucrose gradients). It is generally
desirable to retain the spore populations under non-germinating and
non-growth promoting conditions and media, in order to minimize the
growth of pathogenic bacteria present in the spore populations and
to minimize the germination of spores into vegetative bacterial
cells.
[0086] The compositions of the invention can comprise a carrier
and/or excipient. While it is possible to use a bacterial inoculant
or compound of the present invention for therapy as is, it may be
preferable to administer it in a pharmaceutical formulation, e.g.,
in admixture with a suitable pharmaceutical excipient and/or
carrier selected with regard to the intended route of
administration and standard pharmaceutical practice. The excipient
and/or carrier must be "acceptable" in the sense of being
compatible with the other ingredients of the formulation and not
deleterious to the recipient thereof. Acceptable excipients and
carriers for therapeutic use are well known in the pharmaceutical
art, and are described, for example, in Remington: The Science and
Practice of Pharmacy. Lippincott Williams & Wilkins (A. R.
Gennaro edit. 2005). The choice of pharmaceutical excipient and
carrier can be selected with regard to the intended route of
administration and standard pharmaceutical practice. Oral
formulations readily accommodate additional mixtures, such as,
e.g., milk, yogurt, and infant formula. Solid dosage forms for oral
administration can also be used and can include, e.g., capsules,
tablets, caplets, pills, troches, lozenges, powders, and granules.
Non-limiting examples of suitable excipients include, e.g.,
diluents, buffering agents (e.g., sodium bicarbonate, infant
formula, sterilized human milk, or other agents which allow
bacteria to survive and grow [e.g., survive in the acidic
environment of the stomach and to grow in the intestinal
environment]), preservatives, stabilizers, binders, compaction
agents, lubricants, dispersion enhancers, disintegration agents,
antioxidants, flavoring agents, sweeteners, and coloring agents.
Those of relevant skill in the art are well able to prepare
suitable solutions.
[0087] The bacteria-containing formulations of the invention may
comprise one or more prebiotics which promote growth and/or
activity of the bacteria in the formulation. Non-limiting examples
of prebiotic agents useful in the methods of the present invention
include fructooligosaccharides (e.g., oligofructose, inulin,
inulin-type fructans), galactooligosaccharides, human milk
oligosaccharides (HMO), Lacto-N-neotetraose, D-Tagatose,
xylo-oligosaccharides (XOS), arabinoxylan-oligosaccharides (AXOS),
N-acetylglucosamine, N-acetylgalactosamine, glucose, other five and
six-carbon sugars (e.g., arabinose, maltose, lactose, sucrose,
cellobiose, etc.), amino acids, alcohols, resistant starch (RS),
and mixtures thereof. Additional prebiotic agents can be selected
based on the knowledge of particular bacteria.
[0088] Methods for producing bacterial compositions of the
invention may include three main processing steps, combined with
one or more mixing steps. The steps are: organism banking, organism
production, and preservation. For banking, the strains included in
the bacterial compositions of the invention may be (1) isolated
directly from a specimen or taken from a banked stock, (2)
optionally cultured on a nutrient agar or broth that supports
growth to generate viable biomass, and (3) the biomass optionally
preserved in multiple aliquots in long-term storage. The bacterial
suspension can be freeze-dried to a powder and titrated. After
drying, the powder may be blended to an appropriate potency, and
mixed with other cultures and/or a filler such as microcrystalline
cellulose for consistency and ease of handling, and the bacterial
composition formulated as provided herein.
[0089] Additional methods include methods of evaluating the
microbiota population in a subject or diagnosing an abnormal
microbiota development. Methods include monitoring the infant's
microbiota after the administration of the vaginal microbiota
inoculum or probiotic by: (a) determining a relative abundance of
one or more bacterial taxa in a microbiota sample obtained from the
infant, and (b) comparing the relative abundance(s) determined in
step (a) to (i) a predetermined standard value or (ii) to the
abundance(s) of the same taxa in a control subject or (iii) to the
average value of abundances of the same taxa in several control
subjects. The newborn's sample may be isolated from feces, skin,
oral mucosa, conjunctive mucosa, or nasal mucosa. It may be
compared to a control subject who is a vaginally delivered
full-term healthy infant. The control subject may be born to a
mother who has not been administered antibiotic compounds within a
certain period prior to giving birth (preferably, for at least one
month prior to giving birth), has body mass index (BMI) between
18.5 and 24.9, and does not have irritable bowel disease, Crohn's
disease, ulcerative colitis, irritable bowel syndrome, celiac
disease, colorectal cancer, and a family history of these
diseases.
[0090] The relative abundance of the taxa may comprise a method
selected from the group consisting of quantitative polymerase chain
reaction (qPCR), sequencing of bacterial 16S rRNA, shotgun
metagenome sequencing, and metabolomics.
[0091] In accordance with the present invention there may be
numerous tools and techniques within the skill of the art, such as
those commonly used in molecular biology, pharmacology, and
microbiology. Such tools and techniques are described in detail in
e.g., Sambrook et al. (2001) Molecular Cloning: A Laboratory
Manual. 3rd ed. Cold Spring Harbor Laboratory Press: Cold Spring
Harbor, N.Y.; Ausubel et al. eds. (2005) Current Protocols in
Molecular Biology. John Wiley and Sons, Inc.: Hoboken, N.J.;
Bonifacino et al. eds. (2005) Current Protocols in Cell Biology.
John Wiley and Sons, Inc.: Hoboken, N.J.; Coligan et al. eds.
(2005) Current Protocols in Immunology, John Wiley and Sons, Inc.:
Hoboken, N.J.; Coico et al. eds. (2005) Current Protocols in
Microbiology, John Wiley and Sons, Inc.: Hoboken, N.J.; Coligan et
al. eds. (2005) Current Protocols in Protein Science, John Wiley
and Sons, Inc.: Hoboken, N.J.; and Enna et al. eds. (2005) Current
Protocols in Pharmacology, John Wiley and Sons, Inc.: Hoboken,
N.J.
[0092] In some non-limiting embodiments, the compositions of the
invention are formulated as pharmaceutical preparations for oral,
topical, nasal, rectal, mucosal, sublingual, or nasal
administration. In some embodiments, the formulation is a slow
release formulation. In some embodiments, the compositions are
formulated as medical foods, nutritional or dietary supplements,
food products or beverage products.
EXAMPLES
[0093] The present invention is also described and demonstrated by
way of the following examples. However, the use of these and other
examples anywhere in the specification is illustrative only and in
no way limits the scope and meaning of the invention or of any
exemplified term. Likewise, the invention is not limited to any
particular preferred embodiments described here. Indeed, many
modifications and variations of the invention may be apparent to
those skilled in the art upon reading this specification, and such
variations can be made without departing from the invention in
spirit or in scope. The invention is therefore to be limited only
by the terms of the appended claims along with the full scope of
equivalents to which those claims are entitled.
[0094] The invention provides the following Examples in which
newborns born by C-section were exposed to a gauze that had been
previously introduced in the maternal vagina for one hour prior to
the surgical procedure. The gauze was obtained from healthy mothers
with acidic, Lactobacillus dominant, Group B Streptococcus-negative
vaginas. Newborns were immediately exposed to the gauze at birth,
passing the gauze first through the mouth, then the rest of the
face and body. Swabs from oral, skin, and anal regions were taken
from the baby and the mother (from whom vaginal swabs were also
obtained). Sampling was done at 6 time points during the first
month of life, starting at the day of birth. Bacterial DNA was
extracted and the V4 region of the 16S rRNA gene was sequenced
using an Illumina sequencing instrument. The bacterial microbiota
from the multiple body sites was analyzed using QIIME. Details of
the materials and study designs, as well as the results, are
provided as follows.
Example 1
Transferring Maternal Vaginal Microbiome to Infants Under C-Section
Deliveries
Materials and Methods
Study Design and Enrollment Criteria
[0095] The study protocol was approved by the Institutional Review
Board of the University of Puerto Rico Recinto de Ciencias Medicas
and Rio Piedras campus. Mothers were consented during their 3rd
trimester control OBGYN control visit. There were three groups of
mothers, by delivery and newborn exposure, and they included
vaginal, C-section and C-section with exposure to maternal vaginal
contents. Inclusion criteria included healthy mothers over 21 years
of age, with uncomplicated pregnancies. C-sections were all
scheduled, mostly due to previous C-section or maternal choice. For
the C-section with exposure to maternal vaginal fluids group,
mothers had to have vaginal pH.ltoreq.4 at the time of birth (as
measured with a vaginal swab on pH paper). 18 mothers were
recruited for this preliminary study, 7 of which gave birth
vaginally and 11 by scheduled C-section, of which 4 newborns were
exposed at birth to their mother's vaginal contents (Table 2).
TABLE-US-00003 TABLE 2 Mode and location of delivery of the 20
mothers of the study Perinatal Family # Mode of delivery Birth
Location GBS antibiotics 1 Vaginal Home - - 15 Vaginal Hospital + +
16 Vaginal Hospital - - 19 Vaginal Hospital - - 20 Vaginal Hospital
- - 21 Vaginal Home - - 22 Vaginal Hospital - - 2 Cesarean Hospital
- + 3 Cesarean Hospital - + 4 Cesarean Hospital - + 5 Cesarean
Hospital - + 6 Cesarean Hospital - + 8 Cesarean Hospital - + 9
Cesarean Hospital - + 10 Cesarean Hospital + + 11 Cesarean Hospital
+ + 13 Cesarean + Exposure Hospital - + 14 Cesarean + Exposure
Hospital - + 17 Cesarean + Exposure Hospital - + 18 Cesarean +
Exposure Hospital - +
Procedure of Gauze Exposure in C-Section Babies
[0096] Mothers were sampled before the C-section prophylactic
antibiotics administration. A pair of vaginal swabs were taken, one
to measure fluid pH using pH strip paper (Lab Mikro Hydrion.TM. pH
Test Paper, Fisher 13-640-508). By the time the mother is
administered the preventive antibiotics (1 g Penicillin-family
antibiotics), a medium sterile pad gauze (J&J, 7.6.times.76 cm)
folded like a fan and then in half, was wet with sterile saline
solution and introduced in the maternal birth canal in the hour
prior to the C-section, at the time antibiotics were administered.
The surgeon extracted the gauze right before the procedure, and it
was used to swab the infant just after birth (FIG. 3).
Sample Collection
[0097] Pre-labeled swabs--in duplicate--were taken from 5 body
sites of mother and baby (oral mucosa, forehead, right volar arm,
right foot, and anal) plus two additional from the mother (right
aureole, vagina; Table 3).
TABLE-US-00004 TABLE 3 Number of samples from mothers and infants
Cesarean + C-section Exposure Vaginal Body site N swabs Mother
Infant Mother Infant Mother Infant Total Vaginal 78 32 -- 15 -- 31
-- 78 Aureole 98 39 -- 17 -- 42 -- 98 skin 548 168 104 60 30 93 93
548 anal 226 33 34 14 50 62 33 226 oral 185 42 44 15 35 30 19 185
Total 1057 282 182 106 115 227 145 1057
[0098] Samples were collected from the mother before birth, and
after birth at each timepoint of the mother-baby pair sampling,
namely at .about.day 1, 3, 7, and weekly thereafter to the first
month (Table 2). Vials were maintained cold and frozen at ultralow
temperature (-70 Celsius or below) within the following 2 hours of
collection.
[0099] At each time point at which samples were collected
information survey was applied, and information about mother and
baby health, dietary changes and medications was collected.
16S rRNA Sequencing and Analyses
[0100] Bacterial DNA was extracted from the 1057 swabs, and the V4
region of the 16S rRNA was amplified and sequenced using Illumina
HiSeq as previously described (43). Alpha and beta diversity were
estimated using Qiime (33). Linear Discriminant Analysis Effect
Size (LEfSe) (44) with default parameters was used to determine
taxa that was overrepresented in each baby group in relation to
another.
Results
[0101] Samples from 18 infants and their mothers (Table 1) were
analyzed, including 7 born vaginally and 11 delivered by scheduled
cesarean, of which 4 were exposed to the maternal vaginal fluids at
birth, using a sterile gauze (Table 1). After transferring the
maternal vaginal microbiota to the newborn, the infant microbiota
of the exposed group was compared with those from infants born by
C-section without exposure, during the first month of life.
Briefly, the procedure involved incubating a gauze in the maternal
vagina, for the hour preceding the C-section, in mothers that
complied with inclusion criteria (scheduled C-section, negative
results for GBS, HIV, Chlamydia; vaginal pH<4.5 as measured with
a vaginal swab sample on a pH paper strip). Within the first few
minutes after birth (1-3 min) of these cesarean-delivered infants,
the newborns were exposed to their mother's vaginal contents
swabbing the newborn body, mouth first, then face and rest of the
body (FIG. 1). Of the 14 mothers whose infants were not exposed to
the gauze, 3 were GBS positive, 2 delivering by C-section and 1
delivering vaginally. All mothers who underwent Cesarean section
received perinatal antibiotics, and the one GBS positive mother who
delivered vaginally.
[0102] A total of 1072 swabs from multiple body sites were obtained
from the 18 babies and mothers, during the first month of life (at
1, 3, 7, 14, 21 and 30 days after the birth). Bacterial communities
were characterized by Illumina sequencing of the V4 region of 16S
rRNA gene. Samples that had >1,000 sequences (n=1016) were
further analyzed. A total of 6,515,724 sequences were obtained
(mean 6, (32)3.+-.4,593, median 5,360 sequences), and assigned to
taxa using open reference operational taxonomic unit (OTU) picking
using Qiime (33).
[0103] Body site differentiation of colonized sites in newborns
occurred in as few as 3 days for skin and mouth, but not for in the
whole first month for anal communities (FIG. 2). Regardless of
exposure or birth mode, oral and anal--but not skin--sites showed
the highest bacterial diversity at birth, and alpha diversity
decreased soon after birth (by day 3) in oral and anal sites, and
remained relative stable during the first month of life (FIGS. 3
& 4), when communities seem to converge (FIG. 5). Despite
convergence in whole community structure, major differences
segregate apart the microbiota of infants, by mode of delivery and
exposure.
[0104] The major bacterial markers of delivery present in vaginally
born and not in unexposed Cesarean-delivered infants were i)
Lactobacillus, present in maternal vagina and in all infant sites
at birth, showing a reduction concomitantly with the reduction in
site alpha diversity, during the first 3 days after birth (FIGS. 2
& 6); ii) Bacteroides, Clostridium and Bifidobacterium in anal
swabs; Streptococcus and Staphylococcus in skin and mouth; S24-7
and Stenotrophomonas in skin and oral Veillonella and Gemellaceae,
which bloomed during the first week of the baby life and remained
relatively stable throughout the first month, only in vaginally
born infants (FIG. 2). In contrast, unexposed C-section born babies
had overrepresented anal Veillonella (FIG. 2).
[0105] To identify more specifically bacterial species present in
vaginally born and not in unexposed Cesarean-delivered infants, DNA
was extracted and the V4 region of 16S rRNA gene was sequenced in
Illumina. Sequences were assigned to taxa using BLASTN (web-based
blastn site, NCBI) using OTU picking algorithm, 97% identity to the
Greengenes database (v13_8), in QIIME (Caporaso et al., 2010, Nat.
Methods, 7(5): 335-336). To further confirm taxonomies, the 16S
rRNA sequences of each OTU were used in BLASTN (web-based blastn
suite, NCBI) using 97% identity to the Genbank 16S rRNA sequence
database (MAY2016). The results are shown in Table 4.
TABLE-US-00005 TABLE 4 Species-Level Ideintification of Bacteria
Differentially Observed in Infants by Exposure at Birth BLASTN
Taxonomic info Genus species Identity (%) p_Proteobacteria;
c_Gammaproteobacteria; Acinetobacter 100 o_Pseudomonadales;
f_Moraxellaceae; baumannii g_Acinetobacter; s.sub.--
p_Proteobacteria; c_Gammaproteobacteria; Acinetobacter 100
o_Pseudomonadales; f_Moraxellaceae; gerneri g_Acinetobacter;
s.sub.-- p_Proteobacteria; c_Gammaproteobacteria; Acinetobacter
98.42 o_Pseudomonadales; f_Moraxellaceae; johnsonii
g_Acinetobacter; s_johnsonii p_Proteobacteria;
c_Gammaproteobacteria; Acinetobacter 99.6 o_Pseudomonadales;
f_Moraxellaceae; radioresistens g_Acinetobacter; s.sub.--
p_Proteobacteria; c_Gammaproteobacteria; Acinetobacter 98.42
o_Pseudomonadales; f_Moraxellaceae; schindleri g_Acinetobacter;
s.sub.-- p_Proteobacteria; c_Gammaproteobacteria; Acinetobacter
99.6 o_Pseudomonadales; f_Moraxellaceae; seifertii g_Acinetobacter;
s_rhizosphaerae p_Proteobacteria; c_Gammaproteobacteria;
Acinetobacter 100 o_Pseudomonadales; f_Moraxellaceae; variabilis
g_Acinetobacter; s.sub.-- p_Actinobacteria; c_Actinobacteria;
Actinomyces 100 o_Actinomycetales; f_Actinomycetaceae; europaeus
g_Actinomyces; s_europaeus p_Actinobacteria; c_Actinobacteria;
Actinomyces neuii 100 o_Actinomycetales; f_Actinomycetaceae;
g_Actinomyces; s.sub.-- p_Firmicutes; c_Bacilli; o_Lactobacillales;
Aerococcus 99.21 f_Aerococcaceae; g_Aerococcus; s.sub.--
christensenii p_Actinobacteria; c_Actinobacteria; Alloscardovia 100
o_Bifidobacteriales; f_Bifidobacteriaceae; g_; s.sub.-- omnicolens
p_Firmicutes; c_Clostridia; o_Clostridiales; Anaerococcus 100
f_[Tissierellaceae]; g_Anaerococcus; s.sub.-- lactolyticus
p_Firmicutes; c_Clostridia; o_Clostridiales; Anaerococcus 100
f_[Tissierellaceae]; g_Anaerococcus; s.sub.-- murdochii
p_Firmicutes; c_Clostridia; o_Clostridiales; Anaerococcus 100
f_[Tissierellaceae]; g_Anaerococcus; s.sub.-- obesiensis
p_Firmicutes; c_Clostridia; o_Clostridiales; Anaerococcus 100
f_[Tissierellaceae]; g_Anaerococcus; s.sub.-- octavius
p_Firmicutes; c_Clostridia; o_Clostridiales; Anaerococcus 100
f_[Tissierellaceae]; g_Anaerococcus; s.sub.-- prevotii
p_Firmicutes; c_Clostridia; o_Clostridiales; Anaerococcus 100
f_[Tissierellaceae]; g_Anaerococcus; s.sub.-- provenciensis
p_Firmicutes; c_Clostridia; o_Clostridiales; Anaerococcus 100
f_[Tissierellaceae]; g_Anaerococcus; s.sub.-- vaginalis
p_Firmicutes; c_Clostridia; o_Clostridiales; Anaerostipes hadrus
99.21 f_Lachnospiraceae; g_; s.sub.-- p_Firmicutes; c_Bacilli;
o_Bacillales; Anoxybacillus 100 f_Bacillaceae; g_Anoxybacillus;
s_kestanbolensis flavithermus p_Proteobacteria;
c_Alphaproteobacteria; Asticcacaulis 97.23 o_Caulobacterales;
f_Caulobacteraceae; excentricus g_Asticcacaulis; s.sub.--
p_Actinobacteria; c_Coriobacteriia; Atopobium deltae 99.61
o_Coriobacteriales; f_Coriobacteriaceae; g_Atopobium; s.sub.--
p_Actinobacteria; c_Coriobacteriia; Atopobium vaginae 100
o_Coriobacteriales; f_Coriobacteriaceae; g_; s.sub.-- p_Firmicutes;
c_Bacilli; o_Bacillales; Bacillus vireti 100 f_Bacillaceae;
g_Bacillus; s.sub.-- p_Bacteroidetes; c_Bacteroidia;
o_Bacteroidales; Bacteroides 98.42 f_Bacteroidaceae; g_Bacteroides;
s.sub.-- finegoldii p_Bacteroidetes; c_Bacteroidia;
o_Bacteroidales; Bacteroides vulgatus 100 f_Bacteroidaceae;
g_Bacteroides; s.sub.-- p_Actinobacteria; c_Actinobacteria;
Bifidobacterium 100 o_Bifidobacteriales; f_Bifidobacteriaceae;
breve g_Bifidobacterium; s.sub.-- p_Actinobacteria;
c_Actinobacteria; Bifidobacterium 98.81 o_Bifidobacteriales;
f_Bifidobacteriaceae; pseudolongum g_Bifidobacterium; s.sub.--
p_Proteobacteria; c_Alphaproteobacteria; Blastomonas 100
o_Sphingomonadales; f_Sphingomonadaceae; g_; s.sub.-- natatoria
p_Proteobacteria; c_Alphaproteobacteria; Bradyrhizobium 100
o_Rhizobiales; f_Bradyrhizobiaceae; g_; s.sub.-- lupini
p_Actinobacteria; c_Actinobacteria; Brevibacterium 99.21
o_Actinomycetales; f_Brevibacteriaceae; paucivorans
g_Brevibacterium; s_paucivorans p_Proteobacteria;
c_Epsilonproteobacteria; Campylobacter coli 100
o_Campylobacterales; f_Campylobacteraceae; g_Campylobacter;
s.sub.-- p_Proteobacteria; c_Epsilonproteobacteria; Campylobacter
100 o_Campylobacterales; f_Campylobacteraceae; hominis
g_Campylobacter; s.sub.-- p_Proteobacteria;
c_Epsilonproteobacteria; Campylobacter 100 o_Campylobacterales;
f_Campylobacteraceae; ureolyticus g_Campylobacter; s.sub.--
p_Actinobacteria; c_Actinobacteria; Clavibacter 98.42
o_Actinomycetales; f_Microbacteriaceae michiganensis
p_Bacteroidetes; c_Flavobacteriia; Cloacibacterium 99.21
o_Flavobacteriales; f_[Weeksellaceae]; rupense g_Cloacibacterium;
s.sub.-- p_Firmicutes; c_Clostridia; o_Clostridiales; Clostridium
100 f_Lachnospiraceae; g_; s.sub.-- clostridioforme p_Firmicutes;
c_Clostridia; o_Clostridiales; Clostridium N/A f_Clostridiaceae;
g_Clostridium; s_perfringens perfringens p_Proteobacteria;
c_Betaproteobacteria; Comamonas 99.21 o_Burkholderiales;
f_Comamonadaceae; g_; s.sub.-- serinivorans p_Proteobacteria;
c_Betaproteobacteria; Comamonas 100 o_Burkholderiales;
f_Comamonadaceae; testosteroni g_Comamonas; s.sub.--
p_Actinobacteria; c_Actinobacteria; Corynebacterium 98.43
o_Actinomycetales; f_Corynebacteriaceae; amycolatum
g_Corynebacterium; s.sub.-- p_Actinobacteria; c_Actinobacteria;
Corynebacterium 100 o_Actinomycetales; f_Corynebacteriaceae;
appendicis g_Corynebacterium; s.sub.-- p_Actinobacteria;
c_Actinobacteria; Corynebacterium 99.21 o_Actinomycetales;
f_Corynebacteriaceae; argentoratense g_Corynebacterium; s.sub.--
p_Actinobacteria; c_Actinobacteria; Corynebacterium 100
o_Actinomycetales; f_Corynebacteriaceae; aurimucosum
g_Corynebacterium; s.sub.-- p_Actinobacteria; c_Actinobacteria;
Corynebacterium 99.61 o_Actinomycetales; f_Corynebacteriaceae;
canis g_Corynebacterium; s.sub.-- p_Actinobacteria;
c_Actinobacteria; Corynebacterium 97.24 o_Actinomycetales;
f_Corynebacteriaceae; casei g_Corynebacterium; s.sub.--
p_Actinobacteria; c_Actinobacteria; Corynebacterium 100
o_Actinomycetales; f_Corynebacteriaceae; coyleae g_Corynebacterium;
s.sub.-- p_Actinobacteria; c_Actinobacteria; Corynebacterium 100
o_Actinomycetales; f_Corynebacteriaceae; freneyi g_Corynebacterium;
s.sub.-- p_Actinobacteria; c_Actinobacteria; Corynebacterium 98.82
o_Actinomycetales; f_Corynebacteriaceae; imitans g_Corynebacterium;
s.sub.-- p_Actinobacteria; c_Actinobacteria; Corynebacterium 100
o_Actinomycetales; f_Corynebacteriaceae; jeikeium
g_Corynebacterium; s.sub.-- p_Actinobacteria; c_Actinobacteria;
Corynebacterium 100 o_Actinomycetales; f_Corynebacteriaceae;
kroppenstedtii g_Corynebacterium; s_kroppenstedtii
p_Actinobacteria; c_Actinobacteria; Corynebacterium 100
o_Actinomycetales; f_Corynebacteriaceae; lactis g_Corynebacterium;
s.sub.-- p_Actinobacteria; c_Actinobacteria; Corynebacterium 99.21
o_Actinomycetales; f_Corynebacteriaceae; matruchotii
g_Corynebacterium; s.sub.-- p_Actinobacteria; c_Actinobacteria;
Corynebacterium 98.31 o_Actinomycetales; f_Corynebacteriaceae;
mycetoides g_Corynebacterium; s.sub.-- p_Actinobacteria;
c_Actinobacteria; Corynebacterium 99.61 o_Actinomycetales;
f_Corynebacteriaceae; mycetoides g_Corynebacterium; s.sub.--
p_Actinobacteria; c_Actinobacteria; Corynebacterium 100
o_Actinomycetales; f_Corynebacteriaceae; pilbarense
g_Corynebacterium; s.sub.-- p_Actinobacteria; c_Actinobacteria;
Corynebacterium 100 o_Actinomycetales; f_Corynebacteriaceae;
pyruviciproducens g_Corynebacterium; s.sub.-- p_Actinobacteria;
c_Actinobacteria; Corynebacterium 100 o_Actinomycetales;
f_Corynebacteriaceae; spheniscorum g_Corynebacterium; s.sub.--
p_Actinobacteria; c_Actinobacteria; Corynebacterium 100
o_Actinomycetales; f_Corynebacteriaceae; striatum
g_Corynebacterium; s.sub.-- p_Actinobacteria; c_Actinobacteria;
Corynebacterium 99.21 o_Actinomycetales; f_Corynebacteriaceae;
terpenotabidum g_Corynebacterium; s.sub.-- p_Actinobacteria;
c_Actinobacteria; Corynebacterium 100 o_Actinomycetales;
f_Corynebacteriaceae; thomssenii g_Corynebacterium; s.sub.--
p_Actinobacteria; c_Actinobacteria; Corynebacterium 100
o_Actinomycetales; f_Corynebacteriaceae; tuberculostearicum
g_Corynebacterium; s.sub.-- p_Actinobacteria; c_Actinobacteria;
Corynebacterium 99.61 o_Actinomycetales; f_Corynebacteriaceae;
tuscaniense g_Corynebacterium; s.sub.-- p_Actinobacteria;
c_Actinobacteria; Dermabacter 99.6 o_Actinomycetales;
f_Dermabacteraceae; hominis g_Dermabacter; s.sub.--
p_Actinobacteria; c_Actinobacteria; Devriesea 97.63
o_Actinomycetales; f_Dermabacteraceae agamarum p_Firmicutes;
c_Clostridia; o_Clostridiales; Dialister 100 f_Veillonellaceae;
g_Dialister; s.sub.-- micraerophilus p_Firmicutes; c_Clostridia;
o_Clostridiales; Dialister 100 f_Veillonellaceae; g_Dialister;
s.sub.-- propionicifaciens p_Firmicutes; c_Clostridia;
o_Clostridiales; Dialister 97.62 f_Veillonellaceae; g_Dialister;
s.sub.-- succinatiphilus p_Firmicutes; c_Clostridia;
o_Clostridiales; Dorea longicatena 99.61 f_Lachnospiraceae;
g_[Ruminococcus]; s_gnavus p_Firmicutes; c_Bacilli;
o_Lactobacillales; Enterococcus hirae 100 f_Enterococcaceae;
g_Enterococcus; s.sub.-- p_Firmicutes; c_Bacilli;
o_Lactobacillales; Eremococcus 100 f_Aerococcaceae; g_Facklamia;
s.sub.-- coleocola p_Firmicutes; c_Erysipelotrichi;
Erysipelatoclostridium 100 o_Erysipelotrichales;
f_Erysipelotrichaceae; g_; s.sub.-- ramosum p_Proteobacteria;
c_Gammaproteobacteria; Escherichia 100 o_Enterobacteriales;
f_Enterobacteriaceae; g_; s.sub.-- marmotae p_Firmicutes;
c_Clostridia; o_Clostridiales; Ezakiella peruensis 100
f_[Tissierellaceae]; g_1-68; s.sub.-- p_Firmicutes; c_Bacilli;
o_Lactobacillales; Facklamia hominis 99.21 f_Aerococcaceae;
g_Facklamia; s.sub.-- p_Firmicutes; c_Bacilli; o_Lactobacillales;
Facklamia ignava 100 f_Aerococcaceae; g_Facklamia; s.sub.--
p_Firmicutes; c_Clostridia; o_Clostridiales; Fastidiosipila 99.21
f_Clostridiaceae; g_Clostridium; s.sub.-- sanguinis p_Firmicutes;
c_Clostridia; o_Clostridiales; Fenollaria 100 f_[Tissierellaceae];
g_WAL_1855D; s.sub.-- massiliensis p_Firmicutes; c_Clostridia;
o_Clostridiales; Finegoldia magna 100 f_[Tissierellaceae];
g_Finegoldia; s.sub.-- p_Fusobacteria; c_Fusobacteriia;
Fusobacterium 100 o_Fusobacteriales; f_Fusobacteriaceae; equinum
g_Fusobacterium; s.sub.-- p_Fusobacteria; c_Fusobacteriia;
Fusobacterium 100 o_Fusobacteriales; f_Fusobacteriaceae; nucleatum
g_Fusobacterium; s.sub.-- p_Fusobacteria; c_Fusobacteriia;
Fusobacterium 97.22 o_Fusobacteriales; f_Fusobacteriaceae;
periodonticum g_Fusobacterium; s.sub.-- p_Fusobacteria;
c_Fusobacteriia; Fusobacterium 100 o_Fusobacteriales;
f_Fusobacteriaceae; simiae g_Fusobacterium; s.sub.--
p_Actinobacteria; c_Actinobacteria; Gardnerella 100
o_Bifidobacteriales; f_Bifidobacteriaceae vaginalis p_Firmicutes;
c_Bacilli; o_Gemellales; Gemella 99.6 f_Gemellaceae; g_Gemella;
s.sub.-- asaccharolytica p_Firmicutes; c_Bacilli; o_Gemellales;
Gemella taiwanensis 100 f_Gemellaceae; g_; s.sub.--
p_Proteobacteria; c_Gammaproteobacteria; Haemophilus 100
o_Pasteurellales; f_Pasteurellaceae; pittmaniae g_Aggregatibacter;
s.sub.-- p_Firmicutes; c_Clostridia; o_Clostridiales; Helcococcus
100 f_[Tissierellaceae]; g_Helcococcus; s.sub.-- sueciensis
p_Proteobacteria; c_Betaproteobacteria; Herbaspirillum 100
o_Burkholderiales; f_Oxalobacteraceae chlorophenolicum
p_Synergistetes; c_Synergistia; o_Synergistales; Jonquetella
anthropi 100 f_Dethiosulfovibrionaceae; g_Jonquetella; s_anthropi
p_Actinobacteria; c_Actinobacteria; Kocuria flava strain 98.42
o_Actinomycetales; f_Micrococcaceae; HO-9041 g_Microbispora;
s_rosea p_Actinobacteria; c_Actinobacteria; Kocuria kristinae 100
o_Actinomycetales; f_Micrococcaceae; g_; s.sub.-- strain DSM 20032
p_Actinobacteria; c_Actinobacteria; Kytococcus 99.53
o_Actinomycetales; f_Intrasporangiaceae schroeteri strain Muenster
2000 p_Firmicutes; c_Bacilli; o_Lactobacillales; Lactobacillus 100
f_Lactobacillaceae; g_Lactobacillus; s.sub.-- coleohominis
p_Firmicutes; c_Bacilli; o_Lactobacillales; Lactobacillus 100
f_Lactobacillaceae; g_Lactobacillus; s.sub.-- crispatus
p_Firmicutes; c_Bacilli; o_Lactobacillales; Lactobacillus 100
f_Lactobacillaceae; g_Lactobacillus; s.sub.-- hominis
p_Firmicutes; c_Bacilli; o_Lactobacillales; Lactobacillus iners 100
f_Lactobacillaceae; g_Lactobacillus; s_iners p_Firmicutes;
c_Bacilli; o_Lactobacillales; Lactobacillus 100 f_Lactobacillaceae;
g_Lactobacillus; s.sub.-- intestinalis p_Firmicutes; c_Bacilli;
o_Lactobacillales; Lactobacillus 100 f_Lactobacillaceae;
g_Lactobacillus; s.sub.-- jensenii p_Firmicutes; c_Bacilli;
o_Lactobacillales; Lactobacillus 98.81 f_Lactobacillaceae;
g_Lactobacillus; s.sub.-- psittaci p_Firmicutes; c_Bacilli;
o_Lactobacillales; Lactobacillus reuteri 99.6 f_Lactobacillaceae;
g_Lactobacillus; s.sub.-- p_Firmicutes; c_Bacilli;
o_Lactobacillales; Lactobacillus 97.23 f_Lactobacillaceae;
g_Lactobacillus; s.sub.-- rodentium p_Firmicutes; c_Bacilli;
o_Lactobacillales; Lactococcus lactis 99.6 f_Streptococcaceae;
g_Lactococcus; s.sub.-- p_Firmicutes; c_Clostridia;
o_Clostridiales; Levyella massiliensis 100 f_[Tissierellaceae];
g_ph2; s.sub.-- p_Proteobacteria; c_Betaproteobacteria;
Methylobacillus 100 o_Methylophilales; f_Methylophilaceae
flagellatus p_Proteobacteria; c_Alphaproteobacteria;
Methylobacterium 100 o_Rhizobiales; f_Methylobacteriaceae;
aerolatum g_Methylobacterium p_Proteobacteria;
c_Alphaproteobacteria; Methylobacterium 99.6 o_Rhizobiales;
f_Methylobacteriaceae; phyllostachyos g_Methylobacterium; s.sub.--
p_Actinobacteria; c_Actinobacteria; Micrococcus 100
o_Actinomycetales; f_Micrococcaceae; aloeverae strain AE-
g_Micrococcus; s.sub.-- 6 p_Actinobacteria; c_Actinobacteria;
Mobiluncus curtisii 100 o_Actinomycetales; f_Actinomycetaceae;
g_Mobiluncus; s.sub.-- p_Tenericutes; c_Mollicutes; Mycoplasma 100
o_Mycoplasmatales; f_Mycoplasmataceae; hominis g_Mycoplasma;
s.sub.-- p_Firmicutes; c_Clostridia; o_Clostridiales;
Negativicoccus 100 f_Veillonellaceae succinicivorans
p_Actinobacteria; c_Actinobacteria; Oceanitalea 98.42
o_Actinomycetales; f_Bogoriellaceae; nanhaiensis g_Georgenia;
s.sub.-- p_Bacteroidetes; c_Bacteroidia; o_Bacteroidales;
Parabacteroides 98.42 f_Porphyromonadaceae; g_Parabacteroides;
s.sub.-- faecis p_Bacteroidetes; c_Bacteroidia; o_Bacteroidales;
Parabacteroides 100 f_Porphyromonadaceae; g_Parabacteroides;
s.sub.-- merdae p_Proteobacteria; c_Alphaproteobacteria; Paracoccus
98.81 o_Rhodobacterales; f_Rhodobacteraceae; g_; s.sub.-- communis
p_Firmicutes; c_Clostridia; o_Clostridiales; Parvimonas micra 97.62
f_[Tissierellaceae]; g_Parvimonas; s.sub.-- p_Proteobacteria;
c_Betaproteobacteria; Pelistega indica 99.61 o_Burkholderiales;
f_Alcaligenaceae; g_; s.sub.-- p_Firmicutes; c_Clostridia;
o_Clostridiales; Peptococcus niger 98.81 f_Peptococcaceae;
g_Peptococcus; s.sub.-- p_Firmicutes; c_Clostridia;
o_Clostridiales; Peptoniphilus coxii 100 f_[Tissierellaceae];
g_Peptoniphilus; s.sub.-- p_Firmicutes; c_Clostridia;
o_Clostridiales; Peptoniphilus 100 f_[Tissierellaceae];
g_Peptoniphilus; s.sub.-- duerdenii p_Firmicutes; c_Clostridia;
o_Clostridiales; Peptoniphilus 100 f_[Tissierellaceae];
g_Peptoniphilus; s.sub.-- grossensis p_Firmicutes; c_Clostridia;
o_Clostridiales; Peptoniphilus 99.6 f_[Tissierellaceae];
g_Peptoniphilus; s.sub.-- koenoeneniae p_Firmicutes; c_Clostridia;
o_Clostridiales; Peptoniphilus 100 f_[Tissierellaceae];
g_Peptoniphilus; s.sub.-- lacrimalis p_Firmicutes; c_Clostridia;
o_Clostridiales; Peptoniphilus obesi 98.02 f_[Tissierellaceae];
g_Peptoniphilus; s.sub.-- strain ph1 p_Firmicutes; c_Clostridia;
o_Clostridiales; Peptoniphilus 97.12 f_[Tissierellaceae];
g_Peptoniphilus; s.sub.-- senegalensis p_Firmicutes; c_Clostridia;
o_Clostridiales; Peptoniphilus 100 f_[Tissierellaceae];
g_Peptoniphilus; s.sub.-- tyrrelliae p_Firmicutes; c_Clostridia;
o_Clostridiales; Peptostreptococcus 100 f_Peptostreptococcaceae;
g_Peptostreptococcus; anaerobius s_anaerobius p_Proteobacteria;
c_Betaproteobacteria; Polaromonas sp 99.21 o_Burkholderiales;
f_Comamonadaceae p_Bacteroidetes; c_Bacteroidia; o_Bacteroidales;
Porphyromonas 99.21 f_Porphyromonadaceae; g_Porphyromonas; s.sub.--
bennonis p_Bacteroidetes; c_Bacteroidia; o_Bacteroidales;
Porphyromonas 100 f_Porphyromonadaceae; g_Porphyromonas; s.sub.--
somerae p_Bacteroidetes; c_Bacteroidia; o_Bacteroidales;
Porphyromonas 99.6 f_Porphyromonadaceae; g_Porphyromonas; s.sub.--
uenonis p_Bacteroidetes; c_Bacteroidia; o_Bacteroidales; Prevotella
amnii 99.6 f_Prevotellaceae; g_Prevotella; s.sub.--
p_Bacteroidetes; c_Bacteroidia; o_Bacteroidales; Prevotella
bergensis 100 f_Prevotellaceae; g_Prevotella; s.sub.--
p_Bacteroidetes; c_Bacteroidia; o_Bacteroidales; Prevotella bivia
100 f_Prevotellaceae; g_Prevotella; s.sub.-- p_Bacteroidetes;
c_Bacteroidia; o_Bacteroidales; Prevotella buccalis 99.6
f_Prevotellaceae; g_Prevotella; s.sub.-- p_Bacteroidetes;
c_Bacteroidia; o_Bacteroidales; Prevotella copri 100
f_Prevotellaceae; g_Prevotella; s_copri p_Bacteroidetes;
c_Bacteroidia; o_Bacteroidales; Prevotella corporis 100
f_Prevotellaceae; g_Prevotella; s.sub.-- p_Bacteroidetes;
c_Bacteroidia; o_Bacteroidales; Prevotella disiens 100
f_Prevotellaceae; g_Prevotella; s.sub.-- p_Bacteroidetes;
c_Bacteroidia; o_Bacteroidales; Prevotella 100 f_Prevotellaceae;
g_Prevotella; s.sub.-- timonensis p_Actinobacteria;
c_Actinobacteria; Pseudoclavibacter 99.21 o_Actinomycetales;
f_Microbacteriaceae; bifida strain IAM g_Pseudoclavibacter;
s_bifida 14848 p_Proteobacteria; c_Gammaproteobacteria; Pseudomonas
100 o_Pseudomonadales; f_Pseudomonadaceae; g_; s.sub.-- brenneri
p_Proteobacteria; c_Gammaproteobacteria; Pseudomonas 99.6
o_Pseudomonadales; f_Pseudomonadaceae; helmanticensis
g_Pseudomonas; s.sub.-- p_Proteobacteria; c_Gammaproteobacteria;
Pseudomonas lini 100 o_Pseudomonadales; f_Pseudomonadaceae;
g_Pseudomonas; s.sub.-- p_Proteobacteria; c_Gammaproteobacteria;
Pseudomonas 99.21 o_Pseudomonadales; f_Pseudomonadaceae; syringae
g_Pseudomonas; s.sub.-- p_Actinobacteria; c_Actinobacteria; Rothia
amarae 97.23 o_Actinomycetales; f_Micrococcaceae; g_; s.sub.--
strain J18 p_Actinobacteria; c_Actinobacteria; Rothia mucilaginosa
98.82 o_Actinomycetales; f_Micrococcaceae; g_Rothia; s_mucilaginosa
p_Actinobacteria; c_Rubrobacteria; Rubrobacter 98.42
o_Rubrobacterales; f_Rubrobacteraceae; calidifluminis
g_Rubrobacter; s.sub.-- p_Firmicutes; c_Clostridia;
o_Clostridiales; Ruminococcus 98.43 f_Ruminococcaceae;
g_Ruminococcus; s.sub.-- bromii p_Firmicutes; c_Clostridia;
o_Clostridiales; Ruminococcus 100 f_Lachnospiraceae;
g_[Ruminococcus]; s_gnavus gnavus p_Fusobacteria; c_Fusobacteriia;
Sneathia 100 o_Fusobacteriales; f_Leptotrichiaceae; sanguinegens
g_Sneathia; s.sub.-- p_Proteobacteria; c_Alphaproteobacteria;
Sphingobium 100 o_Sphingomonadales; f_Sphingomonadaceae; yanoikuyae
g_Sphingobium; s.sub.-- p_Proteobacteria; c_Alphaproteobacteria;
Sphingopyxis 99.6 o_Sphingomonadales; f_Sphingomonadaceae;
macrogoltabida g_Sphingopyxis; s.sub.-- p_Firmicutes; c_Bacilli;
o_Bacillales; Staphylococcus 100 f_Planococcaceae; g_; s.sub.--
carnosus p_Firmicutes; c_Bacilli; o_Bacillales; Staphylococcus
97.23 f_Staphylococcaceae; g_Staphylococcus chromogenes
p_Firmicutes; c_Bacilli; o_Bacillales; Staphylococcus 100
f_Staphylococcaceae; g_Staphylococcus; s.sub.-- petrasii
p_Firmicutes; c_Bacilli; o_Bacillales; Staphylococcus 97.23
f_Staphylococcaceae; g_Staphylococcus pseudintermedius
p_Firmicutes; c_Bacilli; o_Bacillales Staphylococcus 100
saprophyticus p_Proteobacteria; c_Gammaproteobacteria;
Stenotrophomonas 98.81 o_Xanthomonadales ; f_Xanthomonadaceae;
maltophilia g_Stenotrophomonas; s.sub.-- p_Firmicutes; c_Bacilli;
o_Lactobacillales; Streptococcus N/A f_Streptococcaceae;
g_Streptococcus; agalactiae s_agalactiae p_Firmicutes; c_Bacilli;
o_Lactobacillales; Streptococcus 100 f_Streptococcaceae;
g_Streptococcus; s.sub.-- agalactiae p_Firmicutes; c_Bacilli;
o_Lactobacillales; Streptococcus 100 f_Streptococcaceae;
g_Streptococcus; anginosus s_anginosus p_Firmicutes; c_Bacilli;
o_Lactobacillales; Streptococcus 97.62 f_Streptococcaceae;
g_Streptococcus; constellatus s_anginosus p_Firmicutes; c_Bacilli;
o_Lactobacillales; Streptococcus 100 f_Streptococcaceae;
g_Streptococcus; s.sub.-- dentisani p_Firmicutes; c_Bacilli;
o_Lactobacillales; Streptococcus 99.6 f_Streptococcaceae;
g_Streptococcus; s.sub.-- lactarius p_Firmicutes; c_Bacilli;
o_Lactobacillales; Streptococcus 99.21 f_Streptococcaceae;
g_Streptococcus; s.sub.-- thermophilus p_Proteobacteria;
c_Betaproteobacteria; Sutterella 99.6 o_Burkholderiales;
f_Alcaligenaceae; stercoricanis g_Sutterella; s.sub.--
p_Tenericutes; c_Mollicutes; Ureaplasma 100 o_Mycoplasmatales;
f_Mycoplasmataceae; urealyticum g_Ureaplasma; s.sub.--
p_Actinobacteria; c_Actinobacteria; Varibaculum 100
o_Actinomycetales; f_Actinomycetaceae; cambriense g_Varibaculum;
s.sub.-- p_Firmicutes; c_Clostridia; o_Clostridiales; Veillonella
dispar 100 f_Veillonellaceae; g_Veillonella; s_dispar p_Firmicutes;
c_Clostridia; o_Clostridiales; Veillonella ratti 99.6
f_Veillonellaceae; g_Veillonella; s.sub.-- p_Firmicutes;
c_Clostridia; o_Clostridiales; f_[Tissierellaceae]; g_1-68;
s.sub.-- p_Firmicutes; c_Clostridia; o_Clostridiales;
f_Veillonellaceae; g_Megasphaera; s.sub.-- p_Fusobacteria;
c_Fusobacteriia; o_Fusobacteriales; f_Leptotrichiaceae;
g_Leptotrichia; s.sub.-- p_Proteobacteria; c_Alphaproteobacteria;
o_Sphingomonadales; f_Sphingomonadaceae; g_Novosphingobium;
s.sub.-- p_Proteobacteria; c_Betaproteobacteria; o_Neisseriales;
f_Neisseriaceae; g_; s.sub.-- p_Proteobacteria;
c_Gammaproteobacteria; o_Xanthomonadales; f_Xanthomonadaceae;
g_Stenotrophomonas; s.sub.--
Example 2
Restoration by Exposure to Vaginal Fluids in C-Section Delivered
Infants
[0106] Since Cesarean-delivered infants were exposed to vaginal
fluids through the use of sterile gauzes, the similarity of the
microbiota of the gauzes to samples obtained from maternal body
sites at day 1 was determined. The gauzes contained vaginal
bacteria such as Lactobacillus, Prevotella, Garnerella, and in less
proportion by Atopobium, Sneathia, Fusobacterium, and Ureoplasma,
and were more similar to the microbiota of maternal vagina, than to
that in other body sites (ANOVA p<0.01).
[0107] Vaginal gauze exposure lead to an infant microbiota closer
to that typical of vaginal than C-section delivery, with partially
restored vaginal markers that were lacking in C-section infants
(FIG. 2, FIG. 6a-6c, Table 5). Major restored bacteria included
Lactobacillus in all infant sites and the early bloom of gut
Bacteroides, oral Gemella, and skin Bacteroidales S24-7 and
Stenotrophomonas. However, these gauze-exposed C-section babies
also showed some markers of C-section delivery, such as high anal
Streptococcus (FIG. 2, Table 5). Random Forest predictions
indicated that mode of delivery could be predicted using oral or
skin microbes. C section birthing was more accurately predicted
than vaginal delivery, and mode of delivery of babies born by
C-section with gauze exposure could not be predicted, indicating an
intermediate composition.
TABLE-US-00006 TABLE 5 Bacteria differentially observed in infants
by exposure at birth Bacterial genus Delivery mode Vaginal Cesarean
Vaginal exposure at + + - birth Infant body site Lactobacillus All
+ + - Bacteroides Anal + + - Clostridium Anal + - - Bifidobacterium
Anal + - - Streptococcus Skin and mouth + - - Staphylococcus Skin
and mouth + - - Bacteroidales S24-7 Skin + + - Stenotrophomonas
Skin + + - Gemellaceae Mouth + + - Streptococcus Anal - - +
Veillonella Anal - - +
[0108] These results demonstrate that babies born vaginally showed
a highly variable microbiota in all body sites (high
inter-individual Unifrac distances), while C-section babies showed
a microbiota with lower variability, similar to that in maternal
skin. C-section babies exposed to maternal inoculum showed
communities resembling more those of the maternal vagina, with
intermediate variability in relation to the other two groups. By
day 30, oral and skin (but not fecal) microbiota clusters with the
corresponding maternal site. Therefore, exposing babies delivered
by C-section to the vaginal microbiota of their mothers partially
restores normal microbial colonization patterns to resemble
vaginally delivered infants.
[0109] The invention thus provides that newborns exposed to the
vaginal canal or gauze, acquire their mother's vaginal bacterial
populations. Blooms of bacteria that occur in newborns are still
associated with maternal bacteria and with feeding mode. Babies are
born with a bacterial diversity that is higher than mother's
vagina, and decreases sharply after birth, presumably due to the
selective pressure of milk. Babies that are breastfed have oral and
skin (forehead and arm) bacterial communities closer to their
mother's (aureole). Feeding mode (breastfed or formula fed) can be
predicted based on the closeness of baby (oral, forehead skin) and
mother's (aureole) bacterial communities. Formula allows higher
colonization of several bacteria such as Leptotrichia.
[0110] It is demonstrated herein that disruption of the natural
birth or feeding process alters significantly the microbiota of
babies, in a crucial developmental stage. Babies born by C-section
can normalize their microbiota (e.g., resemble vaginally delivered
babies) at birth, by being exposed to their mother's vaginal
inoculum. The newborn bacterial diversity of the mouth and anal
microbiota decreases soon after birth, and is maintained remarkably
low during the first month of life. Breast feeding maintains closer
baby-mother microbiota.
Example 3
Determine the Bacteria that Normalizes the Immune and Metabolic
Development in Mice
[0111] The goal of the study is to determine if microbiota of
C-section born infants leads to higher inflammatory response and is
more obesogenic.
[0112] Transfer of whole natural microbiota or mixed or pure
isolates (i) from human maternal vagina or (ii) from meconium/feces
from babies born vaginally are used to determine immune profile and
metabolic responses in GF mice, and are compared to GF mice who
received a transfer of microbiota (iii) from meconium/feces from
babies delivered by C-section.
[0113] The aim is to determine the microbial taxa responsible for
the observed differences, and to optimize for restoring healthy
phenotypes, i.e., minimizing the differences in responses of
C-section related exposures, in relation to the vaginal control
group. The final desired outcome is the alleviation of exposures
that increase the risks of C-section associated disorders, using
microbial exposures natural to mammals.
Example 4
Sequences
[0114] Sequences were obtained for region V4 of the 16S rRNA gene
and compared to the bacterial database "Greenhenes". Taxa were
identified with an identity of >97%. OTUs grouped sequences
sharing more than 97% identity. The data is provided in Table
6.
TABLE-US-00007 TABLE 6 Test- VD_ CS_ Repre- SEQ Time Sta- 1W_ 1W_
sentative ID OTU (weeks) Site tistic P Group mean mean Taxonomy
sequence NO 43935 1 Baby 3.75 0.05 VD 1.4 0 k_Bacteri TACGTAGGGAG 1
32 anal 2807 a;p_Actin CGAGCGTTATC 511 obacteria;c_ CGGATTCATTG
Coriobac GGCGTAAAGAG teriia;o_C CGCGTAGGCGG oriobacteria
CCTCTCAAGCG les;f_Cori GGATCTCTAAT obacteriace CCGAGGGCTCA
ae;g_Egge ACCCCCGGCCG rthella;s_l GATCCCGAACT enta GGGAGGCTCGA
GTTCGGTAGAG GCAGGCGGAAT TCCCGGTGTAG CGGTGGAATGC GCAGATATCGG
GAAGAACACCG ATGGCGAAGGC AGCCTGCTGGG CCGCAACTGAC GCTGAGGCGCG
AAAGCTAGGGG AGCGAACAGG 94711 1 Baby 3.715 0.05 VD 10 0 k_Bacteri
TACGTAGGGTG 2 2 anal 59633 3906 a;p_Actin CGAGCGTTGTC 366
obacteria;c_ CGGAATTACTG Actinoba GGCGTAAAGAG cteria;o_A
CTCGTAGGTGG ctinomycet TTTGTCGCGTC ales;f_Cor GTCTGTGAAAT
ynebacteria TCCGGGGCTTA ceae;g_Co ACTCCGGGCGT rynebacteri
GCAGGCGATAC um;s_ GGGCATAACTT GAGTACTGTAG GGGAGACTGGA ATTCCTGGTGT
AGCGGTGAAAT GCGCAGATATC AGGAGGAACAC CGGTGGCGAAG GCGGGTCTCTG
GGCAGTAACTG ACGCTGAGGAG CGAAAGCATGG GGAGCGAACAG G 44682 1 Baby
3.715 0.05 VD 17.4 0 k_Bacteri TACGGAGGATC 3 34 anal 59633 3906
a;p_Bacte CGAGCGTTATC 366 roidetes;c_ CGGATTTATTG Bacteroidi
GGTTTAAAGGG a;o_Bacte AGCGTAGATGG roidales;f_ ATGTTTAAGTC
Bacteroidac AGTTGTGAAAG eae;g_Bac TTTGCGGCTCA teroides;s_
ACCGTAAAATT GCAGTTGATAC TGGATGTCTTG AGTGCAGTTGA GGCAGGCGGAA
TTCGTGGTGTA GCGGTGAAATG CTTAGATATCA CGAAGAACTCC GATTGCGAAGG
CAGCCTGCTAG GCTGCAACTGA CATTGAGGCTC GAAAGTGTGGG TATCAAACAGG 43768 1
Baby 3.715 0.05 VD 1.2 0 k_Bacteri TACGTAGGGCG 4 28 anal 59633 3906
a;p_Actin CAAGCGTTATC 366 obacteria;c_ CGGATTTATTG Actinoba
GGCGTAAAGGG cteria;o_B CTCGTAGGCGG ifidobacteri CTCGTCGCGTC
ales;f_Bifi CGGTGTGAAAG dobacteriac TCCATCGCTTA eae;g_Bifi
ACGGTGGATCT dobacteriu GCGCCGGGTAC m;s_ GGGCGGGCTTG AGTGCGGTAGG
GGAGACTGGAA TTCCCGGTGTA ACGGTGGAATG TGTAGATATCG GGAAGAACACC
AATGGCGAAGG CAGGTCTCTGG GCCGTTACTGA CGCTGAGGAGC GAAAGCGTGGG
GAGCGAACAGG 57801 1 Baby 3.715 0.05 VD 14.2 0 k_Bacteri TACGGAGGATC
5 6 anal 59633 3906 a;p_Bacte CGAGCGTTATC 366 roidetes;c_
CGGATTTATTG Bacteroidi GGTTTAAAGGG a;o_Bacte TGCGTAGGCGG
roidales;f_ CCTTTTAAGTC Porphyrom AGCGGTGAAAG onadaceae;
TCTGTGGCTCA g_Parabac ACCATAGAATT teroides;s_ GCCGTTGAAAC
distasonis TGGGGGGCTTG AGTATGTTTGA GGCAGGCGGAA TGCGTGGTGTA
GCGGTGAAATG CTTAGATATCA CGCAGAACCCC GATTGCGAAGG CAGCCTGCCAA
GCCATGACTGA CGCTGATGCAC GAAAGCGTGGG GATCAAACAGG 49506 1 Baby 3.715
0.05 VD 19.4 0 k_Bacteri TACGTAGGGTG 6 7 anal 59633 3906 a;p_Actin
CGAGCGTTGTC 366 obacteria;c_ CGGAATTACTG Actinoba GGCGTAAAGAG
cteria;o_A CTCGTAGGCGG ctinomycet TTTGTCACGTC ales;f_Cor
GTCTGTGAAAT ynebacteria CCTAGGGCTTA ceae;g_Co ACCCTGGACGT
rynebacteri GCAGGCGATAC um;s_ GGGCTGACTTG AGTACTACAGG GGAGACTGGAA
TTTCTGGTGTA GCGGTGGAATG CACAGATATCA GGAAGAACACC GATGGCGAAGG
CAGGTCTCTGG GTAGTAACTGA CGCTGAGGAGC GAAAGCATGGG TAGCGAACAGG 11451 1
Baby 3.715 0.05 VD 4.8 0 k_Bacteri TACGGAGGGTG 7 0 anal 59633 3906
a;p_Prote CAAGCGTTAAT 366 obacteria;c_ CGGAATTACTG Gammap
GGCGTAAAGCG roteobacteri CACGCAGGCGG a;o_Enter TTTGTTAAGTC
obacteriales AGATGTGAAAT ;f_Enterob CCCCGGGCTCA acteriaceae;
ACCTGGGAACT g_;s_ GCATCTGATAC TGGCAAGCTTG AGTCTCGTAGA GGGGGGTAGAA
TTCCAGGTGTA GCGGTGAAATG CGTAGAGATCT GGAGGAATACC GGTGGCGAAGG CGG
52680 4 Baby 4.4 0.03 VD 1.6 0 k_Bacteri TACGTAGGTCC 8 4 anal 5938
a;p_Firmi CGAGCGTTATC 931 cutes;c_B CGGATTTATTG acilli;o_L
GGCGTAAAGCG actobacillal AGCGCAGGCGG es;f_Strep TTAGATAAGTC
tococcacea TGAAGTTAAAG e;g_Strept GCTGTGGCTTA ococcus;s_
ACCATAGTACG CTTTGGAAACT GTTTAACTTGA GTGCAGAAGGG GAGAGTGGAAT
TCCATGTGTAG CGGTGAAATGC GTAGATATATG GAGGAACACCG GTGGCGAAAGC
GGCTCTCTGGT CTGTAACTGAC GCTGAGGCTCG AAAGCGTGGGG AGCGAACAGG 10826 4
Baby 4.367 0.03 VD 2.4 0 k_Bacteri TACGTAGGGTG 9 07 anal 64705 6627
a;p_Actin CGAGCGTTGTC 9 535 obacteria;c_ CGGAATTACTG Actinoba
GGCGTAAAGAG cteria;o_A CTCGTAGGCGG ctinomycet TTTGTCACGTC
ales;f_Cor GTCTGTGAAAT ynebacteria CCTAGGGCTTA ceae;g_Co
ACCCTGGACGT rynebacteri GCAGGCGATAC um;s_ GGGCTGACTTG AGTACTACAGG
GGAGACTGGAA TTTCTGGTGTA GCGGTGGAATG CACAGATATCA GGAAGAACACC
GATGGCGAAGG CAGGTCTCTGG GTAGTAACTGA CGCTGAGGAGC GAAAGCATGGG
GAGCGAACAGG 49506 4 Baby 4.367 0.03 VD 22 0 k_Bacteri TACGTAGGGTG
10 7 anal 64705 6627 a;p_Actin CGAGCGTTGTC 9 535 obacteria;c_
CGGAATTACTG Actinoba GGCGTAAAGAG cteria;o_A CTCGTAGGCGG ctinomycet
TTTGTCACGTC ales;f_Cor GTCTGTGAAAT ynebacteria CCTAGGGCTTA
ceae;g_Co ACCCTGGACGT rynebacteri GCAGGCGATAC um;s_ GGGCTGACTTG
AGTACTACAGG GGAGACTGGAA TTTCTGGTGTA GCGGTGGAATG CACAGATATCA
GGAAGAACACC GATGGCGAAGG CAGGTCTCTGG GTAGTAACTGA CGCTGAGGAGC
GAAAGCATGGG TAGCGAACAGG 44252 4 Baby 3.348 0.06 VD 32.6 11
k_Bacteri TACGTAGGTCC 11 14 anal 55403 7264 a;p_Firmi CGAGCGTTGTC 3
075 cutes;c_B CGGATTTATTG acilli;o_L GGCGTAAAGCG actobacillal
AGCGCAGGCGG es;f_Strep TTTGATAAGTC tococcacea TGAAGTTAAAG
e;g_Strept GCTGTGGCTCA
ococcus;s_ ACCATAGTTCG CTTTGGAAACT GTCAAACTTGA GTGCAGAAGGG
GAGAGTGGAAT TCCATGTGTAG CGGTGAAATGC GTAGATATATG GAGGAACACCG
GTGGCGAAAGC GGCTCTCTGGT CTGTAACTGAC GCTGAGGCTCG AAAGCGTGGGG
AGCGAACAGG 44293 4 Baby 2.879 0.08 VD 8.2 0.833 k_Bacteri
TACGTAGGGGG 12 35 anal 52898 9712 33333 a;p_Firmi CTAGCGTTGTC 6 26
3 cutes;c_Cl CGGAATCACTG ostridia;o_ GGCGTAAAGGG Clostridiale
TTCGCAGGCGG s;f_[Tissie AAATGCAAGTC rellaceae];g_ AGGTGTAAAAG
Peptonip GCAGTAGCTTA hilus;s_ ACTACTGTAAG CATTTGAAACT GCATATCTTGA
GAAGAGTAGAG GTAAGTGGAAT TTTTAGTGTAG CGGTGAAATGC GTAGATATTAA
AAAGAATACCG GTGGCGAAGGC GACTTACTGGG CTCATTCTGAC GCTGAGGAACG
AAAGCGTGGGT AGCAAACAGG
REFERENCES
[0115] 1. M. G. Dominguez-Bello, E. K. Costello, M. Contreras, M.
Magris, G. Hidalgo, N. Fierer, R. Knight, Delivery mode shapes the
acquisition and structure of the initial microbiota across multiple
body habitats in newborns. Proc Natl Acad Sci USA 107, 11971-11975
(2010); published online EpubJun 29 (1002601107
[pii]10.1073/pnas.1002601107). [0116] 2. M. Mshvildadze, J. Neu, J.
Shuster, D. Theriaque, N. Li, V. Mai, Intestinal microbial ecology
in premature infants assessed with non-culture-based techniques.
The Journal of pediatrics 156, 20-25 (2010); published online
EpubJan (10.1016/j.jpeds.2009.06.063). [0117] 3. K. Aagaard, J. Ma,
K. M. Antony, R. Ganu, J. Petrosino, J. Versalovic, The placenta
harbors a unique microbiome. Science translational medicine 6,
237ra265 (2014); published online EpubMay 21
(10.1126/scitranslmed.3008599). [0118] 4. K. Aagaard, K. Riehle, J.
Ma, N. Segata, T. A. Mistretta, C. Coarfa, S. Raza, S. Rosenbaum,
I. Van den Veyver, A. Milosavljevic, D. Gevers, C. Huttenhower, J.
Petrosino, J. Versalovic, A metagenomic approach to
characterization of the vaginal microbiome signature in pregnancy.
Plos One 7, e36466 (2012)10.1371/journal.pone.0036466). [0119] 5.
O. Koren, J. K. Goodrich, T. C. Cullender, A. Spor, K. Laitinen, H.
K. Backhed, A. Gonzalez, J. J. Werner, L. T. Angenent, R. Knight,
F. Backhed, E. Isolauri, S. Salminen, R. E. Ley, Host remodeling of
the gut microbiome and metabolic changes during pregnancy. Cell
150, 470-480 (2012); published online EpubAug 3
(10.1016/j.cell.2012.07.008). [0120] 6. A. S. Neish, Microbes in
gastrointestinal health and disease. Gastroenterology 136, 65-80
(2009); published online EpubJan (10.1053/j.gastro.2008.10.080).
[0121] 7. C. Palmer, E. M. Bik, D. B. Digiulio, D. A. Relman, P. O.
Brown, Development of the Human Infant Intestinal Microbiota. Plos
Biol 5, e177 (2007)07-PLBI-RA-0129 [pii]
10.1371/journal.pbio.0050177). [0122] 8. H. R. Gaskins, J. A.
Croix, N. Nakamura, G. M. Nava, Impact of the intestinal microbiota
on the development of mucosal defense. Clinical Infectious Diseases
46, S80-86 (2008). [0123] 9. R. A. Dimmitt, E. M. Staley, G.
Chuang, S. M. Tanner, T. D. Soltau, R. G. Lorenz, Role of Postnatal
Acquisition of the Intestinal Microbiome in the Early Development
of Immune Function. J Pediatr Gastroenterol Nutr, (2010); published
online EpubJul 14 (10.1097/MPG.0b013e3181e1a114). [0124] 10. J. E.
Koenig, A. Spor, N. Scalfone, A. D. Fricker, J. Stombaugh, R.
Knight, L. T. Angenent, R. E. Ley, Succession of microbial
consortia in the developing infant gut microbiome. P Natl Acad Sci
USA 108 Suppl 1, 4578-4585 (2011); published online EpubMar 15
(10.1073/pnas.1000081107). [0125] 11. J. F. Bach, The effect of
infections on susceptibility to autoimmune and allergic diseases.
The New England journal of medicine 347, 911-920 (2002) [0126] 12.
N. T. Mueller, E. Bakacs, J. Combellick, Z. Grigoryan, M. G.
Dominguez-Bello, The infant microbiome development: mom matters.
Trends in molecular medicine 21, 109-117 (2015); published online
EpubFeb (10.1016/j.molmed.2014.12.002). [0127] 13. D. J. Barker,
Human growth and chronic disease: a memorial to Jim Tanner. Annals
of human biology 39, 335-341 (2012); published online EpubSep
(10.3109/03014460.2012.712717). [0128] 14. S. Thavagnanam, J.
Fleming, A. Bromley, M. D. Shields, C. R. Cardwell, A meta-analysis
of the association between Caesarean section and childhood asthma.
Clinical and experimental allergy: journal of the British Society
for Allergy and Clinical Immunology 38, 629-633 (2008); published
online EpubApr (10.1111/j.1365-2222.2007.02780.x). [0129] 15. H.
Renz-Polster, M. R. David, A. S. Buist, W. M. Vollmer, E. A.
O'Connor, E. A. Frazier, M. A. Wall, Caesarean section delivery and
the risk of allergic disorders in childhood. Clinical and
experimental allergy: journal of the British Society for Allergy
and Clinical Immunology 35, 1466-1472 (2005); published online
EpubNov (10.1111/j.1365-2222.2005.02356.x). [0130] 16. C. Roduit,
S. Scholtens, J. C. de Jongste, A. H. Wijga, J. Gerritsen, D. S.
Postma, B. Brunekreef, M. O. Hoekstra, R. Aalberse, H. A. Smit,
Asthma at 8 years of age in children born by caesarean section.
Thorax 64, 107-113 (2009); published online EpubFeb
(10.1136/thx.2008.100875). [0131] 17. M. Pistiner, D. R. Gold, H.
Abdulkerim, E. Hoffman, J. C. Celedon, Birth by cesarean section,
allergic rhinitis, and allergic sensitization among children with a
parental history of atopy. The Journal of allergy and clinical
immunology 122, 274-279 (2008); published online EpubAug
(10.1016/j.jaci.2008.05.007). [0132] 18. S. Hakansson, K. Kallen,
Caesarean section increases the risk of hospital care in childhood
for asthma and gastroenteritis. Clinical and experimental allergy:
journal of the British Society for Allergy and Clinical Immunology
33, 757-764 (2003) [0133] 19. A. Sevelsted, J. Stokholm, K.
Bonnelykke, H. Bisgaard, Cesarean section and chronic immune
disorders. Pediatrics 135, e92-98 (2015); published online EpubJan
(10.1542/peds.2014-0596). [0134] 20. J. Couzin-Frankel, Bacteria
and asthma: untangling the links. Science 330, 1168-1169 (2010);
published online EpubNov 26 (330/6008/1168
[pii]10.1126/science.330.6008.1168). [0135] 21. J. Kero, M.
Gissler, M. M. Gronlund, P. Kero, P. Koskinen, E. Hemminki, E.
Isolauri, Mode of delivery and asthma--is there a connection?
Pediatr Res 52, 6-11 (2002); published online EpubJul
(10.1203/00006450-200207000-00004). [0136] 22. P. Bager, J.
Simonsen, N. M. Nielsen, M. Frisch, Cesarean section and
offspring's risk of inflammatory bowel disease: a national cohort
study. Inflammatory bowel diseases 18, 857-862 (2012); published
online EpubMay (10.1002/ibd.21805). [0137] 23. K. Marild, O.
Stephansson, S. Montgomery, J. A. Murray, J. F. Ludvigsson,
Pregnancy outcome and risk of celiac disease in offspring: a
nationwide case-control study. Gastroenterology 142, 39-45 e33
(2012); published online EpubJan (10.1053/j.gastro.2011.09.047).
[0138] 24. E. Decker, G. Engelmann, A. Findeisen, P. Gerner, M.
Laass, D. Ney, C. Posovszky, L. Hoy, M. W. Hornef, Cesarean
delivery is associated with celiac disease but not inflammatory
bowel disease in children. Pediatrics 125, e1433-1440 (2010);
published online EpubJun (10.1542/peds.2009-2260). [0139] 25. N. T.
Mueller, R. Whyatt, L. Hoepner, S. Oberfield, M. G.
Dominguez-Bello, E. M. Widen, A. Hassoun, F. Perera, A. Rundle,
Prenatal exposure to antibiotics, cesarean section and risk of
childhood obesity. Int J Obes (Lond), (2014); published online
EpubNov 11 (10.1038/ijo.2014.180). [0140] 26. D. N. Mesquita, M. A.
Barbieri, H. A. Goldani, V. C. Cardoso, M. Z. Goldani, G. Kac, A.
A. Silva, H. Bettiol, Cesarean Section Is Associated with Increased
Peripheral and Central Adiposity in Young Adulthood: Cohort Study.
Plos One 8, e66827 (2013)10.1371/journal.pone.0066827). [0141] 27.
L. M. Cox, M. J. Blaser, Pathways in microbe-induced obesity. Cell
metabolism 17, 883-894 (2013); published online EpubJun 4
(10.1016/j.cmet.2013.05.004). [0142] 28. L. M. Cox, S. Yamanishi,
J. Sohn, A. V. Alekseyenko, J. M. Leung, I. Cho, S. G. Kim, H. Li,
Z. Gao, D. Mahana, J. G. Zarate Rodriguez, A. B. Rogers, N. Robine,
P. Loke, M. J. Blaser, Altering the intestinal microbiota during a
critical developmental window has lasting metabolic consequences.
Cell 158, 705-721 (2014); published online EpubAug 14
(10.1016/j.cell.2014.05.052). [0143] 29. I. Cho, S. Yamanishi, L.
Cox, B. A. Methe, J. Zavadil, K. Li, Z. Gao, D. Mahana, K. Raju, I.
Teitler, H. Li, A. V. Alekseyenko, M. J. Blaser, Antibiotics in
early life alter the murine colonic microbiome and adiposity.
Nature 488, 621-626 (2012); published online EpubAug 30
(10.1038/nature11400). [0144] 30. L. M. Cox, M. J. Blaser,
Antibiotics in early life and obesity. Nature reviews.
Endocrinology, (2014); published online EpubDec 9
(10.1038/nrendo.2014.210). [0145] 31. C. Finger, Caesarean section
rates skyrocket in Brazil. Many women are opting for caesareans in
the belief that it is a practical solution. Lancet 362, 628 (2003)
[0146] 32. T. A. Ajslev, C. S. Andersen, M. Gamborg, T. I. A.
Sorensen, T. Jess, Childhood overweight after establishment of the
gut microbiota: the role of delivery mode, pre-pregnancy weight and
early administration of antibiotics. International Journal of
Obesity. 35, 522-529 (2011). [0147] 33. J. G. Caporaso, J.
Kuczynski, J. Stombaugh, K. Bittinger, F. D. Bushman, E. K.
Costello, N. Fierer, A. G. Pena, J. K. Goodrich, J. I. Gordon, G.
A. Huttley, S. T. Kelley, D. Knights, J. E. Koenig, R. E. Ley, C.
A. Lozupone, D. McDonald, B. D. Muegge, M. Pirrung, J. Reeder, J.
R. Sevinsky, P. J. Turnbaugh, W. A. Walters, J. Widmann, T.
Yatsunenko, J. Zaneveld, R. Knight, QIIME allows analysis of
high-throughput community sequencing data. Nature methods 7,
335-336 (2010); published online EpubMay (nmeth.f.303
[pii]10.1038/nmeth.f.303). [0148] 34. H. Ochman, M. Worobey, C. H.
Kuo, J. B. Ndjango, M. Peeters, B. H. Hahn, P. Hugenholtz,
Evolutionary relationships of wild hominids recapitulated by gut
microbial communities. Plos Biol 8, e1000546
(2010)10.1371/journal.pbio.1000546). [0149] 35. P. Soares, L.
Ermini, N. Thomson, M. Mormina, T. Rito, A. Rohl, A. Salas, S.
Oppenheimer, V. Macaulay, M. B. Richards, Correcting for purifying
selection: an improved human mitochondrial molecular clock.
American journal of human genetics 84, 740-759 (2009); published
online EpubJun (10.1016/j.ajhg.2009.05.001). [0150] 36. I. G.
Pantoja-Feliciano, J. C. Clemente, E. K. Costello, M. E. Perez, M.
J. Blaser, R. Knight, M. G. Dominguez-Bello, Biphasic assembly of
the murine intestinal microbiota during early development. The ISME
journal 7, 1112-1115 (2013); published online EpubJun
(10.1038/ismej.2013.15). [0151] 37. OECD, "Health at a Glance 2011:
OECD indicators," (OECD Publishing, 2011). [0152] 38. M. J. Ege, M.
Mayer, A. C. Normand, J. Genuneit, W. O. Cookson, C.
Braun-Fahrlander, D. Heederik, R. Piarroux, E. von Mutius, Exposure
to environmental microorganisms and childhood asthma. The New
England journal of medicine 364, 701-709 (2011); published online
EpubFeb 24 (10.1056/NEJMoa1007302). [0153] 39. C. S. Algert, A.
McElduff, J. M. Morris, C. L. Roberts, Perinatal risk factors for
early onset of Type 1 diabetes in a 2000-2005 birth cohort. Diabet
Med 26, 1193-1197 (2009); published online EpubDec
(10.1111/j.1464-5491.2009.02878.x). [0154] 40. A. Aumeunier, F.
Grela, A. Ramadan, L. Pham Van, E. Bardel, A. Gomez Alcala, P.
Jeannin, S. Akira, J. F. Bach, N. Thieblemont, Systemic Toll-like
receptor stimulation suppresses experimental allergic asthma and
autoimmune diabetes in NOD mice. Plos One 5, e11484
(2010)10.1371/journal.pone.0011484). [0155] 41. S. Y. Huh, S. L.
Rifas-Shiman, C. A. Zera, J. W. Edwards, E. Oken, S. T. Weiss, M.
W. Gillman, Delivery by caesarean section and risk of obesity in
preschool age children: a prospective cohort study. Arch Dis Child
97, 610-616 (2012); published online EpubJul
(10.1136/archdischild-2011-301141). [0156] 42. J. Blustein, T.
Attina, M. Liu, A. Ryan, L. Cox, M. Blaser, L. Trasande,
Association of caesarean delivery with child adiposity from age 6
weeks to 15 years. International Journal of Obesity 37, 900-906
(2013). [0157] 43. J. G. Caporaso, C. L. Lauber, W. A. Walters, D.
Berg-Lyons, J. Huntley, N. Fierer, S. M. Owens, J. Betley, L.
Fraser, M. Bauer, N. Gormley, J. A. Gilbert, G. Smith, R. Knight,
Ultra-high-throughput microbial community analysis on the Illumina
HiSeq and MiSeq platforms. The ISME journal 6, 1621-1624 (2012);
published online EpubAug (10.1038/ismej 0.2012.8). [0158] 44. N.
Segata, J. Izard, L. Waldron, D. Gevers, L. Miropolsky, W. S.
Garrett, C. Huttenhower, Metagenomic biomarker discovery and
explanation. Genome biology 12, R60
(2011)10.1186/gb-2011-12-6-r60). 1. A method for restoring normal
microbiota in an infant delivered by Cesarean section, said method
comprising administering to said infant at the time of birth and/or
within the first 4 months of life an effective amount of a vaginal
microbiota inoculum, wherein said inoculum is obtained from the
subject's mother or from a donor during the third trimester of
pregnancy before or at the time of giving birth. 2. The method of
item 1, wherein the vaginal microbiota inoculum is administered to
the infant within the first 24 hours of life. 3. A method for
restoring normal microbiota in a pre-term infant, said method
comprising administering to said infant at the time of birth and/or
within the first 4 months of life an effective amount of a vaginal
microbiota inoculum, wherein said inoculum is obtained from the
subject's mother or from a donor during the third trimester of
pregnancy before or at the time of giving birth. 4. The method of
item 3, wherein the vaginal microbiota inoculum is administered to
the newborn subject within the first hour of life. 5. A method for
treating a disease in a subject associated with the subject's
delivery by Cesarean section or with the subject's pre-term birth,
said method comprising administering to said subject at the time of
birth and/or within the first 4 months of life a therapeutically
effective amount of a vaginal microbiota inoculum, wherein said
inoculum is obtained from the subject's mother or from a donor
during the third trimester of pregnancy before or at the time of
giving birth. 6. The method of item 5, wherein said disease is an
inflammatory or an autoimmune disorder. 7. The method of item 5,
wherein said disease is selected from the group consisting of
autoimmune diseases, allergic diseases, infectious diseases, and
rejection in organ transplantations. 8. The method of item 5,
wherein said disease is selected from the group consisting of
asthma, allergy, celiac disease, type 1 diabetes, obesity,
necrotizing enterocolitis, inflammatory bowel disease (IBD),
ulcerative colitis, Crohn's disease, sprue, autoimmune arthritis,
rheumatoid arthritis, multiple sclerosis, graft vs. host disease
following bone marrow transplantation, osteoarthritis, juvenile
chronic arthritis, Lyme arthritis, psoriatic arthritis, reactive
arthritis, spondyloarthropathy, systemic lupus erythematosus,
insulin dependent diabetes mellitus, thyroiditis, asthma,
psoriasis, dermatitis scleroderma, atopic dermatitis, graft versus
host disease, acute or chronic immune disease associated with organ
transplantation, sarcoidosis, and atherosclerosis. 9. The method of
any one of items 1-8, wherein the vaginal microbiota inoculum is
delivered to the mouth, nose, and/or skin of the infant. 10. The
method of any one of items 1-8, wherein the vaginal microbiota
inoculum is administered to the infant by a route selected from the
group consisting of oral, topical, rectal, mucosal, sublingual,
nasal, and via naso/oro-gastric gavage. 11. The method of any one
of items 1-10, wherein the vaginal microbiota inoculum is
administered to the infant by placing it on the maternal breast
and/or chest.
12. The method of any one of items 1-11, wherein the vaginal
microbiota inoculum is delivered to the infant in a form of a
liquid, foam, cream, spray, powder, or gel. 13. The method of any
one of items 1-11, wherein the vaginal microbiota inoculum is
delivered to the infant in a form of a composition which comprises
(i) a carrier and/or excipient and/or (ii) one or more prebiotic
agents which stimulate growth and/or activity of one or more
bacteria present in the composition. 14. The method of item 13,
wherein the composition comprises a buffering agent to adjust pH to
the natural vaginal pH at the time of labor or to a pH of 3.5 to 7.
15. The method of item 13 or 14, wherein the composition comprises
an excipient or a carrier that optimizes the seeding of the
transferred microbiota. 16. The method of any one of items 1-15,
wherein the vaginal microbiota inoculum is obtained and/or
delivered using an absorbent material or device. 17. The method of
item 16, wherein the absorbent material or device is selected from
the group consisting of gauze, sponge, and tampon. 18. The method
of item 16 or 17, wherein the vaginal microbiota inoculum is
transferred to said absorbent material or device by introducing
said absorbent material or device in vagina prior to the birth or
at the time of Cesarean section. 19. The method of item 18, wherein
said absorbent material or device is introduced in the vagina for
at least 5 minutes. 20. The method of any one of items 1-19,
wherein said vaginal microbiota inoculum, after it is obtained from
the subject's mother or the donor, is stored in a frozen form. 21.
The method of any one of items 1-20, wherein said vaginal
microbiota inoculum, after it is obtained from the subject's mother
or the donor, is processed to isolate desired bacteria as single or
mixed cultures and such mixed or single cultures are then
administered to the infant. 22. The method of any one of items
1-21, wherein said vaginal microbiota inoculum is lyophilized after
it is obtained from the subject's mother or the donor and
reconstituted prior to the administration to the infant. 23. The
method of any one of items 1-12, wherein prior to obtaining vaginal
microbiota inoculum from the newborn's mother or the donor, it is
verified that said mother or donor does not have Group B
Streptococcus (GBS), human immunodeficiency virus (HIV), and/or
Chlamydia. 24. The method of any one of items 1-23, wherein prior
to obtaining vaginal microbiota inoculum from the newborn's mother
or the donor, it is verified that said mother or donor does not
have sexually transmitted diseases. 25. The method of any one of
items 1-24, wherein prior to obtaining vaginal microbiota from the
newborn's mother or the donor, it is verified that said mother's or
donor's vaginal pH is less than 4.5. 26. The method of any one of
items 1-25, wherein the newborn's mother or the donor has not been
administered antibiotic compounds at least one month prior to the
collection of the microbiota, has body mass index (BMI) between
18.5 and 24.9, and does not have irritable bowel disease, Crohn's
disease, ulcerative colitis, irritable bowel syndrome, celiac
disease, colorectal cancer, and a family history of these diseases.
27. The method of any one of items 1-26, further comprising
monitoring the infant's microbiota after the administration of the
vaginal microbiota inoculum by: (a) determining a relative
abundance of one or more bacterial taxa in a microbiota sample
obtained from the infant, and (b) comparing the relative
abundance(s) determined in step (a) to (i) a predetermined standard
value or (ii) to the abundance(s) of the same taxa in a control
subject or (iii) to the average value of abundances of the same
taxa in several control subjects. 28. The method of item 27,
wherein the infant's microbiota sample is isolated from feces,
skin, oral mucosa, conjunctive mucosa, or nasal mucosa. 29. The
method of item 27 or item 28, wherein the control subject is a
vaginally delivered full-term healthy infant. 30. The method of
item 29, wherein the control subject is born to a mother who has
not been administered antibiotic compounds at least one month prior
to giving birth, has body mass index (BMI) between 18.5 and 24.9,
and does not have irritable bowel disease, Crohn's disease,
ulcerative colitis, irritable bowel syndrome, celiac disease,
colorectal cancer, and a family history of these diseases. 31. The
method of any one of items 27-30, wherein determining the relative
abundance of the bacterial taxa comprises a method selected from
the group consisting of quantitative polymerase chain reaction
(qPCR), sequencing of bacterial 16S rRNA, shotgun metagenome
sequencing, and metabolomics. 32. The method of any one of items
27-31, wherein the bacterial taxa comprise one or more taxa
selected from the group consisting of Lactobacillus, Bacteriodales,
Bacteroides, Parabacteroides, Bacteroidacea, Porphyromonadaceae,
Coriobacteriales, Bifidobacterium, Clostridiaceae,
Stenotrophomonas, and Gemella. 33. The method of item 30, wherein
Bacteriodales is S24-7. 34. The method of any one of items 27-31,
wherein the bacterial taxa comprise one or more taxa recited in
Table 1A. 35. The method of any one of items 27-31, wherein the
bacterial taxa comprise one or more species recited in Table 1B.
36. The method of any one of items 27-31, wherein the bacterial
taxa comprise family Neisseriaceae. 37. A method for restoring
normal microbiota in an infant delivered by Cesarean section, said
method comprising administering to said infant at the time of birth
and/or within the first 4 months of life an effective amount of a
probiotic composition, wherein said probiotic composition (i)
stimulates growth and/or activity of bacteria which are
under-represented in microbiota of said infant as compared to
vaginally delivered full-term infants, and/or (ii) inhibits growth
and/or activity of bacteria which are over-represented in
microbiota of said infant as compared to vaginally delivered
full-term infants. 38. A method for restoring normal microbiota in
a pre-term infant, said method comprising administering to said
infant at the time of birth and/or within the first 4 months of
life an effective amount of a probiotic composition, wherein said
probiotic composition (i) stimulates growth and/or activity of
bacteria which are under-represented in microbiota of said infant
as compared to vaginally delivered full-term infants, and/or (ii)
inhibits growth and/or activity of bacteria which are
over-represented in microbiota of said infant as compared to
vaginally delivered full-term infants. 39. A method for treating a
disease in a subject associated with the subject's delivery by
Cesarean section or with the subject's pre-term birth, said method
comprising administering to said subject at the time of birth
and/or within the first 4 months of life a therapeutically
effective amount of a probiotic composition, wherein said probiotic
composition (i) stimulates growth and/or activity of bacteria which
are under-represented in microbiota of said infant as compared to
vaginally delivered full-term infants, and/or (ii) inhibits growth
and/or activity of bacteria which are over-represented in
microbiota of said infant as compared to vaginally delivered
full-term infants. 40. The method of item 39, wherein said disease
is an inflammatory or an autoimmune disorder. 41. The method of
item 39, wherein said disease is selected from the group consisting
of autoimmune diseases, allergic diseases, infectious diseases, and
rejection in organ transplantations. 42. The method of item 39,
wherein said disease is selected from the group consisting of
asthma, allergy, celiac disease, type 1 diabetes, obesity,
necrotizing enterocolitis, inflammatory bowel disease (IBD),
ulcerative colitis, Crohn's disease, sprue, autoimmune arthritis,
rheumatoid arthritis, multiple sclerosis, graft vs. host disease
following bone marrow transplantation, osteoarthritis, juvenile
chronic arthritis, Lyme arthritis, psoriatic arthritis, reactive
arthritis, spondyloarthropathy, systemic lupus erythematosus,
insulin dependent diabetes mellitus, thyroiditis, asthma,
psoriasis, dermatitis scleroderma, atopic dermatitis, graft versus
host disease, acute or chronic immune disease associated with organ
transplantation, sarcoidosis, and atherosclerosis. 43. The method
of any one of items 37-42, wherein said probiotic composition
comprises one or more bacterial strains from one or more taxa
selected from the group consisting of Lactobacillus, Bacteriodales,
Bacteroides, Parabacteroides, Bacteroidacea, Porphyromonadaceae,
Coriobacteriales, Bifidobacterium, Clostridiaceae,
Stenotrophomonas, and Gemella. 44. The method of item 43, wherein
Bacteriodales is S24-7. 45. The method of any one of items 37-42,
wherein said probiotic composition comprises one or more bacterial
strains from one or more taxa recited in Table 1A. 46. The method
of any one of items 37-42, wherein said probiotic composition
comprises one or more bacterial strains recited in Table 1B. 47.
The method of any one of items 37-42, wherein said probiotic
composition comprises one or more bacterial strains from the family
Neisseriaceae. 48. The method of any one of items 37-47, wherein
said probiotic composition comprises one or more bacterial strains
which can be found in a healthy vaginal microbiota from a pregnant
woman in the third trimester of pregnancy before or at the time of
giving birth. 49. The method of item 48, wherein the woman has not
been administered antibiotic compounds within at least one month
prior to isolation of bacteria, has body mass index (BMI) between
18.5 and 24.9, does not have Group B Streptococcus (GBS), human
immunodeficiency virus (HIV), Chlamydia, and/or sexually
transmitted diseases, has vaginal pH less than 4.5, and does not
have irritable bowel disease, Crohn's disease, ulcerative colitis,
irritable bowel syndrome, celiac disease, colorectal cancer and a
family history of these diseases. 50. The method of any one of
items 37-49, wherein said probiotic composition comprises live
bacterial cells. 51. The method of any one of items 37-49, wherein
said probiotic composition comprises one or more components
selected from the group consisting of conditionally lethal
bacterial cells, inactivated bacterial cells, killed bacterial
cells, spores, recombinant carrier strains, cell extract, and
bacterially-derived products. 52. The method of item 51, wherein
the bacterially-derived product is a bacterial antigen or a
bacterial metabolic product. 53. The method of any one of items
37-52, wherein said probiotic composition comprises (i) a carrier
and/or excipient and/or (ii) one or more prebiotic agents which
stimulate growth and/or activity of one or more bacteria present in
the composition. 54. The method of any one of items 37-53, wherein
said probiotic composition is reconstituted from a lyophilized
preparation. 55. The method of any one of items 37-54, wherein the
probiotic composition comprises a buffering agent to adjust pH to
the natural vaginal pH at the time of labor or to a pH of 3.5 to 7.
56. The method of item 53, wherein the probiotic composition
comprises an excipient or a carrier that optimizes the seeding of
one or more bacterial strains contained in said probiotic
composition. 57. The method of any one of items 37-56, wherein the
probiotic composition is delivered to the mouth, nose, and/or skin
of the infant and/or by placing it on the maternal breast and/or
chest. 58. The method of any one of items 37-56, wherein the
probiotic composition is administered to the infant by a route
selected from the group consisting of oral, topical, rectal,
mucosal, sublingual, nasal, and via naso/oro-gastric gavage. 59.
The method of any one of items 37-58, wherein the probiotic
composition is delivered to the infant in a form of a liquid, foam,
cream, spray, powder, or gel. 60. The method of any one of items
37-59, wherein the probiotic composition is delivered using an
absorbent material or device. 61. The method of item 60, wherein
the absorbent material or device is selected from the group
consisting of gauze, sponge, and tampon. 62. The method of any one
of items 37-60, wherein the probiotic composition comprises a
buffering agent. 63. The method of item 62, wherein the buffering
agent comprises sodium bicarbonate, infant formula or sterilized
human milk. 64. The method of any one of items 37-63, wherein the
probiotic composition is administered conjointly with a prebiotic
which stimulates growth and/or activity of one or more bacteria
contained in the probiotic composition. 65. The method of item 64,
wherein the prebiotic is selected from the group consisting of
fructooligosaccharides (FOS), galactooligosaccharides (GOS), human
milk oligosaccharides (HMO), Lacto-N-neotetraose, D-Tagatose,
xylo-oligosaccharides (XOS), arabinoxylan-oligosaccharides (AXOS),
N-acetylglucosamine, N-acetylgalactosamine, glucose, arabinose,
maltose, lactose, sucrose, cellobiose, amino acids, alcohols,
resistant starch (RS), and any mixtures thereof. 66. The method of
item 64, wherein the prebiotic is derived from microorganisms that
show stimulation by human milk components. 67. The method of any
one of items 64-66, wherein the probiotic and prebiotic are
administered in one composition, or simultaneously as two separate
compositions, or sequentially. 68. A method for diagnosing an
abnormal microbiota development in an infant, comprising: (a)
determining a relative abundance of one or more bacterial taxa in a
microbiota sample obtained from the infant, and (b) comparing the
relative abundance(s) determined in step (a) to (i) a predetermined
standard value or (ii) to the abundance(s) of the same taxa in a
control subject or (iii) to the median value of abundances of the
same taxa in several control subjects, wherein the control subject
is a vaginally delivered full-term healthy infant. 69. The method
of item 68, wherein determining the relative abundance of the
bacterial taxa comprises a method selected from the group
consisting of quantitative polymerase chain reaction (qPCR),
sequencing of bacterial 16S rRNA, shotgun metagenome sequencing,
and metabolomics. 70. The method of item 68 or 69, wherein the
bacterial taxa comprise one or more taxa selected from the group
consisting of Lactobacillus, Bacteriodales, Bacteroides,
Parabacteroides, Bacteroidacea, Porphyromonadaceae,
Coriobacteriales Bifidobacterium, Clostridiaceae, Stenotrophomonas,
and Gemella. 71. The method of item 70, wherein Bacteriodales is
S24-7. 72. The method of item 68 or 69, wherein the bacterial taxa
comprise one or more taxa present in a healthy vaginal microbiota
from a pregnant woman in the third trimester of pregnancy before or
at the time of giving birth. 73. The method of item 68 or 69,
wherein the bacterial taxa comprise one or more taxa recited in
Table 1A. 74. The method of item 68 or 69, wherein the bacterial
taxa comprise one or more species recited in Table 1B.
75. The method of item 68 or 69, wherein the bacterial taxa
comprise family Neisseriaceae. 76. The method of any one of items
1-75, 103, and 104, wherein the infant or subject is human. 77. A
composition comprising (i) a vaginal microbiota inoculum and (ii) a
carrier and/or excipient and/or one or more prebiotic agents which
stimulate growth and/or activity of one or more bacteria present in
the inoculum. 78. A probiotic composition comprising (a) one or
more bacterial strains and (b) a carrier and/or excipient and/or
one or more prebiotic agents which stimulate growth and/or activity
of one or more of said bacterial strains, wherein said probiotic
composition (i) stimulates growth and/or activity of bacteria which
are under-represented in microbiota of an infant delivered by
Cesarean section or born prematurely as compared to vaginally
delivered full-term healthy infants, and/or (ii) inhibits growth
and/or activity of bacteria which are over-represented in
microbiota of said infant as compared to vaginally delivered
full-term healthy infants. 79. The composition of item 78, which
comprises two or more different bacterial strains. 80. The
composition of any one of items 77-79, which comprises bacteria
from one or more taxa selected from the group consisting of
Lactobacillus, Bacteriodales, Bacteroides, Parabacteroides,
Bacteroidacea, Porphyromonadaceae, Coriobacteriales,
Bifidobacterium, Clostridiaceae, Stenotrophomonas, and Gemella. 81.
The composition of item 80, wherein Bacteriodales is S24-7. 82. The
composition of any one of items 77-79, which comprises bacteria
from one or more taxa recited in Table 1A. 83. The composition of
any one of items 77-79, which comprises bacteria from one or more
species recited in Table 1B. 84. The composition of any one of
items 77-79, which comprises bacteria from family Neisseriaceae.
85. The composition of any one of items 77-84, wherein the
composition comprises a buffering agent to adjust pH to the natural
vaginal pH at the time of labor or to a pH of 3.5 to 7. 86. The
composition of any one of items 77-85, wherein the composition
comprises an excipient or a carrier that optimizes the seeding of
one or more bacterial strains contained in the composition. 87. The
composition of any one of items 77-86, wherein said composition is
formulated for storage in a frozen form. 88. The composition of any
one of items 77-87, wherein said composition is a lyophilized
composition. 89. The composition of any one of items 77-88, wherein
said composition comprises one or more bacterial strains which can
be found in a healthy vaginal microbiota from a pregnant woman in
the third trimester of pregnancy before or at the time of giving
birth. 90. The composition of item 89, wherein the woman has not
been administered antibiotic compounds at least one month prior to
isolation of bacteria, has body mass index (BMI) between 18.5 and
24.9, does not have Group B Streptococcus (GBS), human
immunodeficiency virus (HIV), Chlamydia, and/or sexually
transmitted diseases, has vaginal pH less than 4.5, and does not
have irritable bowel disease, Crohn's disease, ulcerative colitis,
irritable bowel syndrome, celiac disease, colorectal cancer or a
family history of these diseases. 91. The composition of any one of
items 77-90, wherein said composition comprises live bacterial
cells. 92. The composition of any one of items 77-90, wherein said
composition comprises one or more components selected from the
group consisting of conditionally lethal bacterial cells,
inactivated bacterial cells, killed bacterial cells, spores,
recombinant carrier strains, cell extract, and bacterially-derived
products. 93. The composition of item 92, wherein the
bacterially-derived product is a bacterial antigen or a bacterial
metabolic product. 94. The composition of any one of items 77-93,
wherein said composition is formulated for delivery to the mouth,
nose, and/or skin of the infant and/or for placing it on the
maternal breast and/or chest. 95. The composition of any one of
items 77-93, wherein said composition is formulated for delivery by
a route selected from the group consisting of oral, topical,
rectal, mucosal, sublingual, nasal, and via naso/oro-gastric
gavage. 96. The composition of any one of items 77-95, wherein the
composition is in a form of a liquid, foam, cream, spray, powder,
or gel. 97. The composition of any one of items 77-96, wherein the
composition comprises a buffering agent. 98. The composition of
item 97, wherein the buffering agent comprises sodium bicarbonate,
infant formula or sterilized human milk. 99. The composition of any
one of items 77-98, wherein the composition comprises a prebiotic
which stimulates growth and/or activity of one or more bacteria
contained in the composition. 100. The method of item 99, wherein
the prebiotic is selected from the group consisting of
fructooligosaccharides (FOS), galactooligosaccharides (GOS), human
milk oligosaccharides (HMO), Lacto-N-neotetraose, D-Tagatose,
xylo-oligosaccharides (XOS), arabinoxylan-oligosaccharides (AXOS),
N-acetylglucosamine, N-acetylgalactosamine, glucose, arabinose,
maltose, lactose, sucrose, cellobiose, amino acids, alcohols,
resistant starch (RS), and any mixtures thereof. 101. An absorbent
material or device comprising the composition of any one of items
77-100. 102. The material or device of item 101, wherein the
material or device is selected from the group consisting of gauze,
sponge, and tampon. 103. A method for restoring normal microbiota
in an infant delivered by Cesarean section, said method comprising
administering to said infant at the time of birth and/or within the
first 4 months of life an effective amount of the composition of
any one of items 77-100. 104. A method for restoring normal
microbiota in a pre-term infant, said method comprising
administering to said infant at the time of birth and/or within the
first 4 months of life an effective amount of the composition of
any one of items 77-100. 105. A method for treating a disease in a
subject associated with the subject's delivery by Cesarean section
or with the subject's pre-term birth, said method comprising
administering to said subject at the time of birth and/or within
the first 4 months of life a therapeutically effective amount of
the composition of any one of items 77-100. 106. The method of item
105, wherein the subject is human. 107. The method of any one of
items 1-76, 103 and 104, wherein the infant is a newborn.
[0159] The present invention is not to be limited in scope by the
specific embodiments described herein. Indeed, various
modifications of the invention in addition to those described
herein will become apparent to those skilled in the art from the
foregoing description. Such modifications are intended to fall
within the scope of the appended claims.
[0160] All patents, applications, publications, test methods,
literature, and other materials cited herein are hereby
incorporated by reference in their entirety as if physically
present in this specification.
Sequence CWU 1
1
121252DNAEggerthella lenta 1tacgtaggga gcgagcgtta tccggattca
ttgggcgtaa agagcgcgta ggcggcctct 60caagcgggat ctctaatccg agggctcaac
ccccggccgg atcccgaact gggaggctcg 120agttcggtag aggcaggcgg
aattcccggt gtagcggtgg aatgcgcaga tatcgggaag 180aacaccgatg
gcgaaggcag cctgctgggc cgcaactgac gctgaggcgc gaaagctagg
240ggagcgaaca gg 2522254DNACorynebacterium sp. 2tacgtagggt
gcgagcgttg tccggaatta ctgggcgtaa agagctcgta ggtggtttgt 60cgcgtcgtct
gtgaaattcc ggggcttaac tccgggcgtg caggcgatac gggcataact
120tgagtactgt aggggagact ggaattcctg gtgtagcggt gaaatgcgca
gatatcagga 180ggaacaccgg tggcgaaggc gggtctctgg gcagtaactg
acgctgagga gcgaaagcat 240ggggagcgaa cagg 2543253DNABacteroides sp.
3tacggaggat ccgagcgtta tccggattta ttgggtttaa agggagcgta gatggatgtt
60taagtcagtt gtgaaagttt gcggctcaac cgtaaaattg cagttgatac tggatgtctt
120gagtgcagtt gaggcaggcg gaattcgtgg tgtagcggtg aaatgcttag
atatcacgaa 180gaactccgat tgcgaaggca gcctgctagg ctgcaactga
cattgaggct cgaaagtgtg 240ggtatcaaac agg 2534253DNABifidobacterium
sp. 4tacgtagggc gcaagcgtta tccggattta ttgggcgtaa agggctcgta
ggcggctcgt 60cgcgtccggt gtgaaagtcc atcgcttaac ggtggatctg cgccgggtac
gggcgggctt 120gagtgcggta ggggagactg gaattcccgg tgtaacggtg
gaatgtgtag atatcgggaa 180gaacaccaat ggcgaaggca ggtctctggg
ccgttactga cgctgaggag cgaaagcgtg 240gggagcgaac agg
2535253DNAParabacteroides distasonis 5tacggaggat ccgagcgtta
tccggattta ttgggtttaa agggtgcgta ggcggccttt 60taagtcagcg gtgaaagtct
gtggctcaac catagaattg ccgttgaaac tggggggctt 120gagtatgttt
gaggcaggcg gaatgcgtgg tgtagcggtg aaatgcttag atatcacgca
180gaaccccgat tgcgaaggca gcctgccaag ccatgactga cgctgatgca
cgaaagcgtg 240gggatcaaac agg 2536253DNACorynebacterium sp.
6tacgtagggt gcgagcgttg tccggaatta ctgggcgtaa agagctcgta ggcggtttgt
60cacgtcgtct gtgaaatcct agggcttaac cctggacgtg caggcgatac gggctgactt
120gagtactaca ggggagactg gaatttctgg tgtagcggtg gaatgcacag
atatcaggaa 180gaacaccgat ggcgaaggca ggtctctggg tagtaactga
cgctgaggag cgaaagcatg 240ggtagcgaac agg
2537201DNAUnknownDescription of Unknown Enterobacteriaceae
polynucleotide 7tacggagggt gcaagcgtta atcggaatta ctgggcgtaa
agcgcacgca ggcggtttgt 60taagtcagat gtgaaatccc cgggctcaac ctgggaactg
catctgatac tggcaagctt 120gagtctcgta gaggggggta gaattccagg
tgtagcggtg aaatgcgtag agatctggag 180gaataccggt ggcgaaggcg g
2018252DNAStreptococcus sp. 8tacgtaggtc ccgagcgtta tccggattta
ttgggcgtaa agcgagcgca ggcggttaga 60taagtctgaa gttaaaggct gtggcttaac
catagtacgc tttggaaact gtttaacttg 120agtgcagaag gggagagtgg
aattccatgt gtagcggtga aatgcgtaga tatatggagg 180aacaccggtg
gcgaaagcgg ctctctggtc tgtaactgac gctgaggctc gaaagcgtgg
240ggagcgaaca gg 2529253DNACorynebacterium sp. 9tacgtagggt
gcgagcgttg tccggaatta ctgggcgtaa agagctcgta ggcggtttgt 60cacgtcgtct
gtgaaatcct agggcttaac cctggacgtg caggcgatac gggctgactt
120gagtactaca ggggagactg gaatttctgg tgtagcggtg gaatgcacag
atatcaggaa 180gaacaccgat ggcgaaggca ggtctctggg tagtaactga
cgctgaggag cgaaagcatg 240gggagcgaac agg 25310253DNACorynebacterium
sp. 10tacgtagggt gcgagcgttg tccggaatta ctgggcgtaa agagctcgta
ggcggtttgt 60cacgtcgtct gtgaaatcct agggcttaac cctggacgtg caggcgatac
gggctgactt 120gagtactaca ggggagactg gaatttctgg tgtagcggtg
gaatgcacag atatcaggaa 180gaacaccgat ggcgaaggca ggtctctggg
tagtaactga cgctgaggag cgaaagcatg 240ggtagcgaac agg
25311252DNAStreptococcus sp. 11tacgtaggtc ccgagcgttg tccggattta
ttgggcgtaa agcgagcgca ggcggtttga 60taagtctgaa gttaaaggct gtggctcaac
catagttcgc tttggaaact gtcaaacttg 120agtgcagaag gggagagtgg
aattccatgt gtagcggtga aatgcgtaga tatatggagg 180aacaccggtg
gcgaaagcgg ctctctggtc tgtaactgac gctgaggctc gaaagcgtgg
240ggagcgaaca gg 25212252DNAPeptoniphilus sp. 12tacgtagggg
gctagcgttg tccggaatca ctgggcgtaa agggttcgca ggcggaaatg 60caagtcaggt
gtaaaaggca gtagcttaac tactgtaagc atttgaaact gcatatcttg
120agaagagtag aggtaagtgg aatttttagt gtagcggtga aatgcgtaga
tattaaaaag 180aataccggtg gcgaaggcga cttactgggc tcattctgac
gctgaggaac gaaagcgtgg 240gtagcaaaca gg 252
* * * * *